bpforms/alphabet/protein.yml
id: protein
name: Protein amino acids
description: The canonical protein amino acids, plus non-canonical amino acids based
on <a href="http://www.wwpdb.org/data/ccd">PDB Chemical Component Dictionary</a>
and <a href="https://pir.georgetown.edu/resid">RESID</a>
monomers:
A:
id: Ala
name: L-alanine
synonyms:
- (S)-alpha-Amino-beta-phenylpropionic acid
- L-alanine
- alanine
- (S)-2-Amino-3-phenylpropionic acid
- 3-phenyl-L-alanine
- β-phenyl-L-alanine
- (2S)-2-aminopropanoic acid
- A
identifiers:
- ns: pdb-ccd
id: ALA
- ns: metacyc.compound
id: L-ALPHA-ALANINE
- ns: resid
id: AA0001
- ns: chebi
id: CHEBI:46217
- ns: chebi
id: CHEBI:16977
- ns: pubchem.compound
id: '5950'
structure: C[C@H]([NH3+])C(=O)O
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
- molecule: Monomer
element: H
position: 4
charge: 1
R:
id: Arg
name: L-arginine
synonyms:
- (S)-alpha-Amino-beta-phenylpropionic acid
- arginine
- '[amino-[[(4S)-4-amino-5-hydroxy-5-oxo-pentyl]amino]methylidene]azanium'
- amino{[(4S)-4-amino-4-carboxybutyl]amino}methaniminium
- (S)-2-Amino-3-phenylpropionic acid
- 3-phenyl-L-alanine
- β-phenyl-L-alanine
- R
identifiers:
- ns: chebi
id: CHEBI:16467
- ns: pubchem.compound
id: '6322'
- ns: metacyc.compound
id: ARG
- ns: pdb-ccd
id: ARG
- ns: chebi
id: CHEBI:29952
- ns: resid
id: AA0002
structure: OC(=O)[C@H](CCCNC(=[NH2+])N)[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
charge: 1
- molecule: Monomer
element: H
position: 15
N:
id: Asn
name: L-asparagine
synonyms:
- L-Asparagine
- L-aspartic acid beta-amide
- L-Asparagin
- asparagine
- (2S)-2,4-diamino-4-oxobutanoic acid
- L-asparagine
- (S)-Asparagine
- L-2-aminosuccinamic acid
- N
- (2S)-2,4-bis(azanyl)-4-oxidanylidene-butanoic acid
- Aspartamic acid
- (2S)-2-amino-3-carbamoylpropanoic acid
- (S)-2-amino-3-carbamoylpropanoic acid
- alpha-aminosuccinamic acid
- 2-Aminosuccinamic acid
identifiers:
- ns: pdb-ccd
id: ASN
- ns: chebi
id: CHEBI:17196
- ns: metacyc.compound
id: ASN
- ns: resid
id: AA0003
- ns: chebi
id: CHEBI:50347
- ns: pubchem.compound
id: '6267'
structure: NC(=O)C[C@@H](C(=O)O)[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
charge: 1
- molecule: Monomer
element: H
position: 10
D:
id: Asp
name: L-aspartic acid
synonyms:
- D
- (S)-2-aminosuccinic acid
- L-aspartic acid
- 2-Aminosuccinic acid
- (2S)-2-azanylbutanedioic acid
- aspartic acid
- (S)-2-aminobutanedioic acid
- L-Asparaginsaeure
identifiers:
- ns: resid
id: AA0004
- ns: pdb-ccd
id: ASP
- ns: pubchem.compound
id: '5960'
- ns: metacyc.compound
id: ASP
- ns: chebi
id: CHEBI:17053
- ns: chebi
id: CHEBI:29958
structure: O=C[C@H](CC(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
C:
id: Cys
name: L-cysteine
synonyms:
- (2R)-2-amino-3-sulfanylpropanoic acid
- E 920
- E-920
- L-Zystein
- E920
- (2R)-2-amino-3-mercaptopropanoic acid
- (R)-2-amino-3-mercaptopropanoic acid
- L-2-Amino-3-mercaptopropionic acid
identifiers:
- ns: chebi
id: CHEBI:17561
- ns: resid
id: AA0005
- ns: pubchem.compound
id: '5862'
- ns: chebi
id: CHEBI:29950
- ns: metacyc.compound
id: CYS
structure: OC(=O)[C@@H]([NH3+])CS
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
Q:
id: Gln
name: L-glutamine
synonyms:
- (2S)-2,5-diamino-5-oxopentanoic acid
- L-(+)-glutamine
- Glutamic acid 5-amide
- (2S)-2,5-diamino-5-oxo-pentanoic acid
- Glutamic acid amide
- glutamine
- L-2-Aminoglutaramic acid
- L-glutamine
- (2S)-2-amino-4-carbamoylbutanoic acid
- Levoglutamide
- L-2-aminoglutaramic acid
- L-glutamic acid gamma-amide
- L-Glutaminsaeure-5-amid
- (S)-2,5-diamino-5-oxopentanoic acid
- Q
identifiers:
- ns: resid
id: AA0007
- ns: pubchem.compound
id: '5961'
- ns: chebi
id: CHEBI:18050
- ns: pdb-ccd
id: GLN
- ns: chebi
id: CHEBI:30011
- ns: metacyc.compound
id: GLN
structure: NC(=O)CC[C@@H](C(=O)O)[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
E:
id: Glu
name: L-glutamic acid
synonyms:
- (S)-glutamic acid
- (2S)-2-azanylpentanedioic acid
- L-glutamic acid
- E
- (S)-2-aminopentanedioic acid
- L-Glutaminic acid
- glutamic acid
- L-Glutaminsaeure
- Glutamate
identifiers:
- ns: resid
id: AA0006
- ns: pubchem.compound
id: '33032'
- ns: chebi
id: CHEBI:29972
- ns: metacyc.compound
id: GLU
- ns: chebi
id: CHEBI:16015
- ns: pdb-ccd
id: GLU
structure: O=C[C@H](CCC(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
G:
id: Gly
name: glycine
synonyms:
- aminoethanoic acid
- Aminoacetic acid
identifiers:
- ns: chebi
id: CHEBI:29947
- ns: resid
id: AA0008
- ns: metacyc.compound
id: GLY
- ns: chebi
id: CHEBI:15428
- ns: pubchem.compound
id: '750'
structure: OC(=O)C[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
H:
id: His
name: L-histidine
synonyms:
- histidine
- L-(-)-histidine
- (2S)-2-amino-3-(1H-imidazol-3-ium-4-yl)propanoic acid
- H
- (S)-alpha-amino-1H-Imidazole-4-propanoic acid
- (S)-4-(2-Amino-2-carboxyethyl)imidazole
- 3-(1H-imidazol-3-ium-4-yl)-L-alanine
- (S)-alpha-Amino-1H-imidazole-4-propionic acid
identifiers:
- ns: pdb-ccd
id: HIS
- ns: resid
id: AA0009
- ns: pubchem.compound
id: '33032'
- ns: chebi
id: CHEBI:29979
- ns: metacyc.compound
id: HIS
- ns: chebi
id: CHEBI:15971
structure: OC(=O)[C@@H]([NH3+])Cc1cnc[nH]1
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
I:
id: Ile
name: L-isoleucine
synonyms:
- alpha-amino-beta-methylvaleric acid
- I
- (2S,3S)-2-amino-3-methyl-pentanoic acid
- L-isoleucine
- (2S,3S)-2-amino-3-methylpentanoic acid
- 2-Amino-3-methylvaleric acid
- isoleucine
identifiers:
- ns: pubchem.compound
id: '6306'
- ns: pdb-ccd
id: ILE
- ns: metacyc.compound
id: ILE
- ns: chebi
id: CHEBI:17191
- ns: resid
id: AA0010
- ns: chebi
id: CHEBI:30009
structure: CC[C@@H]([C@@H](C(=O)O)[NH3+])C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
L:
id: Leu
name: L-leucine
synonyms:
- L-leucine
- (2S)-alpha-Leucine
- (2S)-2-amino-4-methylpentanoic acid
- (2S)-2-amino-4-methyl-pentanoic acid
- leucine
- 2-Amino-4-methylvaleric acid
- L
- (S)-leucine
- (2S)-alpha-2-Amino-4-methylvaleric acid
- (S)-(+)-leucine
identifiers:
- ns: chebi
id: CHEBI:15603
- ns: pubchem.compound
id: '6106'
- ns: metacyc.compound
id: LEU
- ns: chebi
id: CHEBI:30006
- ns: pdb-ccd
id: LEU
- ns: resid
id: AA0011
structure: '[NH3+][C@H](C(=O)O)CC(C)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
K:
id: Lys
name: L-lysine
synonyms:
- 6-ammonio-L-norleucine
- K
- lysine
- '[(5S)-5-amino-6-hydroxy-6-oxo-hexyl]azanium'
identifiers:
- ns: chebi
id: CHEBI:18019
- ns: pubchem.compound
id: '5962'
- ns: resid
id: AA0012
- ns: metacyc.compound
id: LYS
- ns: pdb-ccd
id: LYS
- ns: chebi
id: CHEBI:29967
structure: '[NH3+]CCCC[C@@H](C(=O)O)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
M:
id: Met
name: L-methionine
synonyms:
- (2S)-2-amino-4-(methylsulfanyl)butanoic acid
- (S)-methionine
- (2S)-2-amino-4-methylsulfanyl-butanoic acid
- (S)-2-amino-4-(methylthio)butyric acid
- (S)-2-amino-4-(methylthio)butanoic acid
- L-alpha-amino-gamma-methylmercaptobutyric acid
- methionine
- M
- L-methionine
- L-(-)-methionine
identifiers:
- ns: metacyc.compound
id: MET
- ns: resid
id: AA0013
- ns: pdb-ccd
id: MET
- ns: chebi
id: CHEBI:16044
- ns: chebi
id: CHEBI:16643
- ns: pubchem.compound
id: '6137'
structure: CSCC[C@H]([NH3+])C(=O)O
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
F:
id: Phe
name: L-phenylalanine
synonyms:
- (S)-alpha-Amino-beta-phenylpropionic acid
- (S)-2-Amino-3-phenylpropionic acid
- 3-phenyl-L-alanine
- F
- β-phenyl-L-alanine
- (2S)-2-amino-3-phenyl-propanoic acid
- L-phenylalanine
- phenylalanine
identifiers:
- ns: pubchem.compound
id: '22848660'
- ns: pdb-ccd
id: PHE
- ns: chebi
id: CHEBI:29997
- ns: metacyc.compound
id: PHE
- ns: resid
id: AA0014
- ns: chebi
id: CHEBI:17295
structure: '[NH3+][C@H](C(=O)O)Cc1ccccc1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
P:
id: Pro
name: L-proline
synonyms:
- (S)-pyrrolidine-2-carboxylic acid
- L-proline
- L-(-)-proline
- (S)-2-carboxypyrrolidine
- L-alpha-pyrrolidinecarboxylic acid
- (-)-proline
- L-pyrrolidine-2-carboxylic acid
- (S)-2-pyrrolidinecarboxylic acid
- proline
- P
- (-)-(S)-proline
- (2S)-pyrrolidine-2-carboxylic acid
- 2-Pyrrolidinecarboxylic acid
- (-)-2-pyrrolidinecarboxylic acid
identifiers:
- ns: resid
id: AA0015
- ns: chebi
id: CHEBI:17203
- ns: metacyc.compound
id: PRO
- ns: chebi
id: CHEBI:50342
- ns: pubchem.compound
id: '145742'
- ns: pdb-ccd
id: PRO
structure: OC(=O)[C@@H]1CCC[NH2+]1
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
S:
id: Ser
name: L-serine
synonyms:
- L-serine
- L-2-Amino-3-hydroxypropionic acid
- (2S)-2-amino-3-hydroxypropanoic acid
- (S)-2-amino-3-hydroxypropanoic acid
- (S)-serine
- (S)-(-)-serine
- (2S)-2-amino-3-hydroxy-propanoic acid
- L-(-)-serine; beta-Hydroxyalanine
- L-3-Hydroxy-alanine
- S
- serine
- (S)-alpha-Amino-beta-hydroxypropionic acid
- L-3-Hydroxy-2-aminopropionic acid
- beta-Hydroxy-L-alanine
identifiers:
- ns: chebi
id: CHEBI:17115
- ns: chebi
id: CHEBI:29999
- ns: resid
id: AA0016
- ns: metacyc.compound
id: SER
- ns: pubchem.compound
id: '5951'
- ns: pdb-ccd
id: SER
structure: OC[C@@H](C(=O)O)[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
- molecule: Monomer
element: H
position: 7
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
T:
id: Thr
name: L-threonine
synonyms:
- threonine
- 2-Amino-3-hydroxybutyric acid
- T
- L-(-)-Threonine
- L-threonine
- (2S,3R)-2-amino-3-hydroxybutanoic acid
- (2S,3R)-(-)-Threonine
- L-2-Amino-3-hydroxybutyric acid
- (2S,3R)-2-amino-3-hydroxy-butanoic acid
- L-alpha-amino-beta-hydroxybutyric acid
- (2S)-threonine
identifiers:
- ns: pdb-ccd
id: THR
- ns: metacyc.compound
id: THR
- ns: pubchem.compound
id: '6288'
- ns: resid
id: AA0017
- ns: chebi
id: CHEBI:30013
- ns: chebi
id: CHEBI:16857
structure: C[C@H]([C@@H](C(=O)O)[NH3+])O
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
- molecule: Monomer
element: H
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
W:
id: Trp
name: L-tryptophan
synonyms:
- (S)-α-amino-1H-indole-3-propanoic acid
- (S)-tryptophan
- tryptophan
- L-(−)-tryptophan
- (S)-alpha-Amino-beta-(3-indolyl)-propionic acid
- W
- (2S)-2-amino-3-(1H-indol-3-yl)propanoic acid
- L-tryptophan
- L-β-3-indolylalanine
identifiers:
- ns: chebi
id: CHEBI:29954
- ns: pdb-ccd
id: TRP
- ns: resid
id: AA0018
- ns: metacyc.compound
id: TRP
- ns: pubchem.compound
id: '6305'
- ns: chebi
id: CHEBI:16828
structure: OC(=O)[C@H](Cc1c[nH]c2c1cccc2)[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
Y:
id: Tyr
name: L-tyrosine
synonyms:
- (S)-2-Amino-3-(p-hydroxyphenyl)propionic acid
- (-)-alpha-amino-p-hydroxyhydrocinnamic acid
- 4-hydroxy-L-phenylalanine
- L-tyrosine
- (S)-Tyrosine
- (S)-3-(p-Hydroxyphenyl)alanine
- (2S)-2-amino-3-(4-hydroxyphenyl)propanoic acid
- tyrosine
- Y
- (S)-(-)-Tyrosine
- (S)-alpha-amino-4-hydroxybenzenepropanoic acid
identifiers:
- ns: pdb-ccd
id: TYR
- ns: chebi
id: CHEBI:46858
- ns: resid
id: AA0019
- ns: chebi
id: CHEBI:17895
- ns: metacyc.compound
id: TYR
- ns: pubchem.compound
id: '6057'
structure: OC(=O)[C@H](Cc1ccc(cc1)O)[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
V:
id: Val
name: L-valine
synonyms:
- (S)-valine
- 2-Amino-3-methylbutyric acid
- V
- L-(+)-alpha-Aminoisovaleric acid
- (2S)-2-amino-3-methylbutanoic acid
- valine
- L-valine
- (2S)-2-amino-3-methyl-butanoic acid
- L-alpha-Amino-beta-methylbutyric acid
identifiers:
- ns: chebi
id: CHEBI:30015
- ns: metacyc.compound
id: VAL
- ns: resid
id: AA0020
- ns: pubchem.compound
id: '6287'
- ns: chebi
id: CHEBI:16414
- ns: pdb-ccd
id: VAL
structure: '[NH3+]C(C(=O)O)C(C)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
- molecule: Monomer
element: H
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
charge: 1
- molecule: Monomer
element: H
position: 1
AA0318:
id: AA0318
name: L-lysine methyl ester
comments: 'Generating Enzyme: protein-lysine O-methyltransferase (EC 2.1.1.-).'
synonyms:
- 2,6-diaminohexanoic methyl ester
- methyl L-lysinate
- methyl (S)-2,6-diaminohexanoate
- alpha,epsilon-diaminocaproic methyl ester
identifiers:
- ns: mod
id: MOD:00323
- ns: go
id: GO:0042034
- ns: cas
id: 687-64-9
- ns: chebi
id: CHEBI:21354
- ns: resid
id: AA0318
structure: COC(=O)[C@@H]([NH3+])CCCC[NH3+]
base_monomers:
- K
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
AA0567:
id: AA0567
name: N6-(2-butenonyl)-L-lysine
comments: A metabolic source for crotonic acid or crotonyl-CoA in the nucleus
is not evident, and a responsible enzyme activity is not identified.
synonyms:
- N6-crotonyllysine
- N6-[(2E)-2-butenoyl]-L-lysine
- N(epsilon)-crotonyllysine
- N6-(E)-crotonyllysine
- (2S)-2-amino-6-[(2E)-but-2-enoylamino]hexanoic acid
- (2S)-2-azanyl-6-[(2E)-but-2-enoylazanyl]hexanoic acid
- N6-trans-crotonyllysine
- (2S)-2-amino-6-[(2E)-but-2-enamido]hexanoic acid
identifiers:
- ns: resid
id: AA0567
- ns: mod
id: MOD:01892
structure: C/C=C/C(=O)NCCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0037:
id: AA0037
name: O-phospho-L-serine
comments: 'Generating Enzyme: protein-serine kinase (EC 2.7.1.37).'
synonyms:
- (2S)-2-amino-3-phosphonooxy-propanoic acid
- serine phosphate ester
- O3-phosphoserine
- 2-azanyl-3-(phosphonooxy)propanoic acid
- (2S)-2-amino-3-(phosphonooxy)propanoic acid
- 2-amino-3-hydroxypropanoic acid 3-phosphate
- O-phosphonoserine
- phosphoserine
- O-phosphono-L-serine
- S
identifiers:
- ns: resid
id: AA0037
- ns: pdb-ccd
id: SEP
- ns: mod
id: MOD:00046
- ns: chebi
id: CHEBI:45522
- ns: cas
id: 407-41-0
- ns: go
id: GO:0018105
- ns: pdb.ligand
id: SEP
structure: OC(=O)[C@H](COP(=O)([O-])[O-])[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
AA0048:
id: AA0048
name: N2-acetyl-L-lysine
comments: The occurrence of this modification has not been confirmed. The common
peptide alpha-N-acetyltransferase does not acetylate basic residues.
synonyms:
- 2-acetylazanyl-6-azanylhexanoic acid
- N2-acetyllysine
- 2-acetylamino-6-aminohexanoic acid
- (2S)-2-acetamido-6-aminohexanoic acid
identifiers:
- ns: mod
id: MOD:00057
- ns: resid
id: AA0048
- ns: go
id: GO:0017195
- ns: cas
id: 1946-82-3
structure: CC(=O)N[C@H](C(=O)O)CCCC[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
M, W, Y:
id: AA0348
name: S-[5'-(L-tryptoph-6'-yl)-L-tyrosin-3'-yl]-L-methionin-S-ium
comments: This modification is produced auto-catalytically.
synonyms:
- 5'-(6'-tryptophyl)-tyrosin-3'-yl-methionin-S-ium
identifiers:
- ns: go
id: GO:0050739
- ns: resid
id: AA0348
- ns: mod
id: MOD:00353
structure: O=C[C@H](CC[S@](c1cc(C[C@@H](C(=O)O)N)cc(c1O)c1ccc2c(c1)[nH]cc2C[C@@H](C=O)N)C)N
base_monomers:
- W
- M
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
- molecule: Monomer
element: H
position: 16
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
AA0421:
id: AA0421
name: N4-glucosyl-L-asparagine
comments: The alpha anomeric form is shown. See also RESID:AA0151 and RESID:AA0420
for other N4-glycosylated asparagines.
synonyms:
- (2S)-2-amino-4-(D-glucopyranosyl)amino-4-oxobutanoic acid
- N4-glycosylasparagine
- N4-(D-glucopyranosyl)-L-asparagine
- N4-glycosyl-L-asparagine
- N4-asparagine-glucoside
- N4-glucosylasparagine
identifiers:
- ns: mod
id: MOD:00833
- ns: resid
id: AA0421
structure: OC[C@H]1O[C@H](NC(=O)C[C@@H](C(=O)O)N)[C@@H]([C@H]([C@@H]1O)O)O
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
- molecule: Monomer
element: H
position: 16
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
AA0560:
id: AA0560
name: S-(N-acetylamino)glucosyl-L-cysteine
comments: See also RESID:AA0152 and RESID:AA0392 for other S-glycosylated cysteines.
synonyms:
- S-[beta-D-(N-acetylamino)glucopyranosyl]cysteine
- (2R)-2-amino-3-(2-acetamido-2-deoxy-beta-D-glucopyranosylsulfanyl)propanoic
acid
- S-[(N-acetylamino)glycosyl]cysteine
identifiers:
- ns: chebi
id: CHEBI:61631
- ns: cas
id: 10036-64-3
- ns: mod
id: MOD:01858
- ns: resid
id: AA0560
structure: OC[C@H]1O[C@@H](SC[C@@H](C(=O)O)[NH3+])[C@@H]([C@H]([C@@H]1O)O)NC(=O)C
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0172:
id: AA0172
name: O4'-sulfo-L-tyrosine
comments: 'Generating Enzyme: protein-tyrosine sulfotransferase (EC 2.8.2.20).'
synonyms:
- (2S)-2-azanyl-3-(4-sulfooxyphenyl)propanoic acid
- tyrosine-O-sulphonic acid
- 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-sulfate
- tyrosine sulfate
- O4-sulfotyrosine
- Y
- tyrosine-O-sulfonic acid
- o-sulfo-l-tyrosine
- O-sulfo-L-tyrosine
- (S)-2-amino-3-(4-sulfooxyphenyl)propanoic acid
identifiers:
- ns: pdb.ligand
id: TYS
- ns: pdb-ccd
id: TYS
- ns: go
id: GO:0006478
- ns: cas
id: 956-46-7
- ns: resid
id: AA0172
- ns: mod
id: MOD:00181
structure: OC(=O)[C@H](Cc1ccc(cc1)OS(=O)(=O)[O-])[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0231:
id: AA0231
name: N4-(ADP-ribosyl)-L-asparagine
comments: 'It is not known whether botulinum exoenzyme C3 catalyzes formation
of the alpha or beta isomer. The alpha form is presented. The keyword "phosphoprotein"
is not used with toxin modification. Generating Enzyme: NAD(P)+--asparagine
ADP-ribosyltransferase (EC 2.4.2.-).'
synonyms:
- N4-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-asparagine
- (S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-4-oxobutanoic
acid
- N4-alpha-D-ribofuranosyl-L-asparagine 5'->5'-ester with adenosine 5'-(trihydrogen
diphosphate)
identifiers:
- ns: mod
id: MOD:00236
- ns: go
id: GO:0006471
- ns: resid
id: AA0231
structure: O=C(N[C@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)(OP(=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)[O-])[O-])C[C@@H](C(=O)O)N
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 50
l_bond_atoms:
- molecule: Monomer
element: N
position: 53
r_displaced_atoms:
- molecule: Monomer
element: O
position: 52
- molecule: Monomer
element: H
position: 52
l_displaced_atoms:
- molecule: Monomer
element: H
position: 53
AA0150:
id: AA0150
name: O3-phosphopantetheine-L-serine
comments: 'Generating Enzyme: holo-[acyl-carrier-protein] synthase (EC 2.7.8.7).'
synonyms:
- (2R)-2-hydroxy-3,3-dimethyl-4-[(2S)-2-amino-2-carboxyethyl]phosphonato-N-(3-oxo-3-[(2-sulfanylethyl)amino]propyl)butanamide
identifiers:
- ns: pdb.ligand
id: PNS
- ns: mod
id: MOD:00159
- ns: resid
id: AA0150
- ns: go
id: GO:0018070
structure: SCCNC(=O)CCNC(=O)[C@H](C(COP(=O)(OC[C@@H](C(=O)O)[NH3+])[O-])(C)C)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 23
l_bond_atoms:
- molecule: Monomer
element: N
position: 26
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 25
- molecule: Monomer
element: H
position: 25
l_displaced_atoms:
- molecule: Monomer
element: H
position: 26
- molecule: Monomer
element: H
position: 26
charge: 1
AA0238:
id: AA0238
name: L-cysteine oxazole-4-carboxylic acid
comments: 'Formed by the condensation of a serine hydroxyl with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-serine
cyclase (EC 4.2.1.-); peptidyl-oxazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-(1-azanyl-2-sulfanylethyl)-4-oxazolecarboxylic acid
- 2-[(1R)-1-amino-2-sulfanylethyl]-1,3-oxazole-4-carboxylic acid
identifiers:
- ns: resid
id: AA0238
- ns: go
id: GO:0018132
- ns: mod
id: MOD:00243
structure: N[C@H](c1nc(co1)C(=O)O)CS
base_monomers:
- S
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
- molecule: Monomer
element: H
position: 11
AA0062:
id: AA0062
name: N,N,N-trimethyl-L-alanine
comments: 'Consult FAQ at http://pir.georgetown.edu/resid/faq.shtml#q12 concerning
calculation of the difference formula. Generating Enzyme: ribosomal protein
L11 methyltransferase prmA (EC 2.1.1.-); N-terminal RCC1 methyltransferase (EC
2.1.1.-).'
synonyms:
- (1S)-1-carboxy-N,N,N-trimethylethanaminium
- N,N,N-trimethylalaninium
- (1S)-1-carboxy-N,N,N-trimethylethanazanium
- N,N,N-trimethylalanine cation
- (2S)-2-(trimethylammonio)propanoic acid
identifiers:
- ns: go
id: GO:0018011
- ns: resid
id: AA0062
- ns: mod
id: MOD:00071
- ns: cas
id: 44802-94-0
structure: C[C@H]([N](C)(C)C)C(=O)O
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
AA0177:
id: AA0177
name: 3',3'',5'-triiodo-L-thyronine
synonyms:
- 4-(4-hydroxy-3-iodophenoxy)-3,5-diiodo-L-phenylalanine
- T3
- O-(4-hydroxy-3-iodophenyl)-3,5-diiodo-L-tyrosine
- liothyronine
- 3,5,3'-triiodo-L-thyronine
- 3,3',5-triiodo-L-thyronine
- (S)-2-amino-3-[4-(4-hydroxy-3-iodophenoxy)-3,5-diiodophenyl]propanoic acid
identifiers:
- ns: cas
id: 6893-02-3
- ns: pdb.ligand
id: T3
- ns: go
id: GO:0018078
- ns: chebi
id: CHEBI:18258
- ns: resid
id: AA0177
- ns: mod
id: MOD:00186
structure: OC(=O)[C@H](Cc1cc(I)c(c(c1)I)Oc1ccc(c(c1)I)O)[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 24
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 24
- molecule: Monomer
element: H
position: 24
charge: 1
AA0530:
id: AA0530
name: N6-(lysyl)-L-Lysine
comments: 'This modification occurs transiently in prokaryotic elogation factor
P during production of the mature protein. For the mature form of the EF-P modification,
see RESID:AA0531. The modified lysine residue is homologous to the lysine modified
to hypusine (see RESID:AA0116) in eukaryotic and archaeal translation initiation
factor 5A. Generating Enzyme: translation elongation factor P-lysine N6-lysyltransferase
YjeA (EC 2.3.2.-).'
synonyms:
- (2S)-2-amino-6-([(2S)-2,6-diaminohexanoyl]amino)hexanoic acid
- N6-(alpha-lysyl)-lysine
identifiers:
- ns: mod
id: MOD:01779
- ns: go
id: GO:0071915
- ns: resid
id: AA0530
structure: '[NH3+]CCCC[C@@H](C(=O)NCCCC[C@@H](C(=O)O)[NH3+])[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 23
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: H
position: 23
- molecule: Monomer
element: H
position: 23
charge: 1
AA0577:
id: AA0577
name: O4'-(N-acetylamino)galactosyl-L-tyrosine
comments: 'The alpha anomeric form is shown. See also RESID:AA0157 for other O-glycosylated
tyrosines. Generating Enzyme: polypeptide N-acetylgalactosaminyltransferase
(EC 2.4.1.-).'
synonyms:
- mucin type O-glycosyltyrosine
- (2S)-2-amino-3-(D-2-acetamido-2-deoxygalactopyranosyloxy)phenylpropanoic acid
- O4'-glycosyl-L-tyrosine
- O4'-(N-acetylgalactosaminyl)tyrosine
identifiers:
- ns: resid
id: AA0577
- ns: mod
id: MOD:01916
structure: OC[C@@H]1O[C@H](Oc2ccc(cc2)C[C@@H](C(=O)O)[NH3+])[C@H]([C@H]([C@H]1O)O)NC(=O)C
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
- molecule: Monomer
element: H
position: 20
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
AA0611:
id: AA0611
name: S-(gamma-glutamyl-cysteinyl-glycyl)-L-cysteine
comments: 'Generating Enzyme: autocatalytic.'
synonyms:
- (2S)-2-amino-5-([(2R)-1-([2-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-2-oxoethyl]amino)-1-oxo-3-sulfanylpropan-2-yl]amino)-5-oxopentanoic
acid
- S-(glutathion-1-yl)-L-cysteine
identifiers:
- ns: mod
id: MOD:01969
- ns: resid
id: AA0611
structure: O=C[C@H](CSC(=O)CNC(=O)[C@H](NC(=O)CC[C@@H](C(=O)[O-])[NH3+])CS)N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 22
l_bond_atoms:
- molecule: Monomer
element: N
position: 25
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 25
- molecule: Monomer
element: H
position: 25
charge: 1
AA0133:
id: AA0133
name: S-phytochromobilin-L-cysteine
comments: The phytochromobilins and phycoerythrobilins transmit red.
synonyms:
- 18-ethenyl-3-[1-((2-amino-2-carboxy)ethylsulfanyl)ethyl]-1,2,3,19,22,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic
acid
- (2R,3R)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-18-ethyl-2,7,13,17-tetramethyl-1,2,3,19,21,22,24-heptahydrobilin-1,19(21H,22H,24H)-dione
- phytochrome chromophore
- phytochromobilin cysteine adduct
identifiers:
- ns: cas
id: 143392-71-6
- ns: go
id: GO:0017012
- ns: mod
id: MOD:00142
- ns: resid
id: AA0133
- ns: chebi
id: CHEBI:15619
structure: O=C[C@H](CS[C@@H]([C@H]1/C(=C/[C@H]2[NH2+]/C(=C\c3[nH]c(c(c3CCC(=O)[O-])C)/C=C/3\NC(=O)C(=C3C)C=C)/C(=C2C)CCC(=O)[O-])/NC(=O)[C@H]1C)C)[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 28
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0084:
id: AA0084
name: L-aspartic acid 1-amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- l-alpha-asparagine
- alpha-asparagine
- 3,4-diamino-4-oxobutanoic acid
- (2S)-2-amino-1-butanediamic acid
- isoasparagine
- N
- (3S)-3,4-bis(azanyl)-4-oxidanylidene-butanoic acid
- L-alpha-asparagine
- 3-amino-succinamic acid
identifiers:
- ns: go
id: GO:0018037
- ns: mod
id: MOD:00093
- ns: chebi
id: CHEBI:49010
- ns: resid
id: AA0084
- ns: cas
id: 498-25-9
- ns: pdb-ccd
id: XSN
- ns: pdb.ligand
id: NH2
structure: '[O-]C(=O)C[C@@H](C(=O)N)[NH3+]'
base_monomers:
- N
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
AA0333:
id: AA0333
name: S-cyano-L-cysteine
comments: This modification is produced naturally when the HypE protein undergoes
an auto-catalyzed dehydration, using ATP, of its carboxy-terminal S-carbamoyl
cysteine. See RESID:AA0332.
synonyms:
- serine thiocyanic acid ester
- S-cyano-L-cysteine
- alpha-amino-beta-thiocyanatopropionic acid
- (2R)-2-amino-3-thiocyanatopropanoic acid
- C
- beta-thiocyanatoalanine
- S-cyanocysteine
- (2R)-2-azanyl-3-thiocyanato-propanoic acid
- s-cyano-l-cysteine
identifiers:
- ns: go
id: GO:0046892
- ns: pdb-ccd
id: XCN
- ns: mod
id: MOD:00338
- ns: resid
id: AA0333
- ns: cas
id: 5652-31-3
structure: N[C@H](C(=O)O)CSC#N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0344:
id: AA0344
name: 4-amino-3-isothiazolidinone-L-serine
comments: 'This cross-link is formed by the condensation of a cysteine sulfenic
acid with the alpha-amido of the following residue. It can apparently be reversed
by simple disulfhydryl reduction under physiological conditions. Generating
Enzyme: autocatalytic.'
synonyms:
- (2S)-2-[(4R)-4-amino-3-oxo-1,2-thiazolidin-2-yl]-3-hydroxypropanoic acid
- 2-(4-amino-3-oxo-isothiazolidin-2-yl)-3-hydroxy-propanoic acid
- serine-cysteine sulphenyl amide cross-link
- 4-amino-3-isothiazolidinone-L-serine
- serine-cysteine sulfenyl amide cross-link
identifiers:
- ns: resid
id: AA0344
- ns: go
id: GO:0048109
- ns: mod
id: MOD:00349
structure: OC[C@H](N1SC[C@@H](C1=O)[NH3+])C(=O)O
base_monomers:
- S
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
- molecule: Monomer
element: H
position: 18
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
AA0088:
id: AA0088
name: glycine amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- 2-azanylethanamide
- glycinamide
- 2-aminoethanamide
- 2-aminoacetamide
identifiers:
- ns: mod
id: MOD:00097
- ns: chebi
id: CHEBI:42843
- ns: cas
id: 598-41-4
- ns: resid
id: AA0088
- ns: pdb.ligand
id: NH2
- ns: go
id: GO:0018041
structure: NC(=O)C[NH3+]
base_monomers:
- G
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0290:
id: AA0290
name: O-octanoyl-L-serine
comments: 'Generating Enzyme: ghrelin O-acyltransferase, GOAT (EC 2.3.1.-).'
synonyms:
- L-serine octanoate ester
- (2S)-2-amino-3-(octanoyloxy)propanoic acid
- O3-octanoyl-L-serine
identifiers:
- ns: go
id: GO:0018191
- ns: mod
id: MOD:00295
- ns: resid
id: AA0290
structure: CCCCCCCC(=O)OC[C@@H](C(=O)O)[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
- molecule: Monomer
element: H
position: 16
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
AA0526:
id: AA0526
name: S-(coelenterazin-3a-yl)-L-cysteine
comments: 'Coelenterazine is one of the four major marine luciferins, being used
by various bioluminescent species in at least eight phyla. Coelenterazine may
result from modification of a phenylalanyl-tyrosyl-tyrosine peptide produced
by an unidentified endosymbiotic organism. See RESID:AA0595. The chirality
of the cysteine adduct has not been determined. This entry presents coelenterazine
as a heterogen cross-linked to a cysteine. For coelenterazine as a modification
produced by the cross-linking of a tripeptide precursor see RESID:AA0595. Generating
Enzyme: autocatalytic.'
synonyms:
- symplectin chromophore
- dehydrocoelenterazine cysteine adduct
- (2R)-2-amino-3-([(4-hydroxyphenyl)(8-benzyl-3-oxo-6-[4-hydroxyphenyl]-3,7-dihydroimidazo[1,2-a]pyrazin-2-yl)methyl]sulfanyl)propanoic
acid
identifiers:
- ns: resid
id: AA0526
- ns: cas
id: 55779-48-1
- ns: chebi
id: CHEBI:2311
- ns: mod
id: MOD:01694
structure: Oc1ccc(cc1)[C@H](c1nc2n(c1=O)cc([nH]c2Cc1ccccc1)c1ccc(cc1)O)SC[C@@H](C(=O)O)[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 39
l_bond_atoms:
- molecule: Monomer
element: N
position: 42
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 41
- molecule: Monomer
element: H
position: 41
l_displaced_atoms:
- molecule: Monomer
element: H
position: 42
- molecule: Monomer
element: H
position: 42
charge: 1
AA0059:
id: AA0059
name: N-myristoyl-glycine
comments: 'The myristyl group represents a mixture of saturated and unsaturated
fatty acids. Depending on the membrane composition, fatty acids including C12:0,
C14:0, C14:1, and C14:2 may be incorporated. This modification is usually co-translational,
occurring as the protein N-terminal emerges from the ribosome and immediately
after the initial methionine is cleaved. However, glycine myristoylation can
in some cases be performed on an N-terminal glycine produced by a post-translational
proteolytic cleavage. The ExPASy Prosite pattern PS00008 should only be used
with extreme caution. Because that pattern is not anchored to an N-terminal
glycine, it extravagantly overpredicts "myristoylation" sites throughout the
entire length of many protein sequences. Glycine myristoylation can only occur
once in any protein sequence - at the N-terminal. Generating Enzyme: glycylpeptide
N-tetradecanoyltransferase (EC 2.3.1.97).'
synonyms:
- N-tetradecanoylglycine
- (tetradecanoylamino)ethanoic acid
- N-myristylglycine
- N-(1-oxotetradecyl)glycine
identifiers:
- ns: go
id: GO:0018008
- ns: resid
id: AA0059
- ns: pdb.ligand
id: MYR
- ns: cas
id: 14246-55-0
- ns: mod
id: MOD:00068
structure: CCCCCCCCCCCCCC(=O)NCC(=O)O
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
- molecule: Monomer
element: H
position: 20
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
AA0119:
id: AA0119
name: N6-pyridoxal phosphate-L-lysine
synonyms:
- 2-azanyl-6-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic
acid
- (2s)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic
acid
- (E)-N~6~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-lysine
- K
- (2S)-2-amino-6-[([3-hydroxy-2-methyl-5-phosphonooxymethylpyridin-4-yl]methylidene)amino]hexanoic
acid
identifiers:
- ns: go
id: GO:0018272
- ns: cas
id: 2440-59-7
- ns: resid
id: AA0119
- ns: mod
id: MOD:00128
- ns: pdb-ccd
id: LLP
- ns: pdb.ligand
id: LLP
structure: OC(=O)[C@H](CCCC[NH2+]Cc1c(cnc(c1O)C)COP(=O)([O-])[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 28
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 28
- molecule: Monomer
element: H
position: 28
charge: 1
AA0494:
id: AA0494
name: N-(DNA-1',2'-dideoxyribos-1'-ylidene)-L-prolinium
comments: "The modification is frequently referred to as a \"Schiff base\". As\
\ an iminium bonded to three carbons, this is not a Schiff base, defined in\
\ the IUPAC Compendium of Chemical Terminology, 2nd ed. (\"the Gold Book\",\
\ http://goldbook.iupac.org/index.html) as an imine (uncharged, double bonded\
\ nitrogen) bonded to two carbons. Chemically it is not a \"base\" because it\
\ cannot act as either a proton acceptor (a \"Brønsted-Lowry base\") or as\
\ an electron pair donor (a \"Lewis base\"). The model has three open valences,\
\ one on the proline carboxyl group and two in the DNA nucleotide segment on\
\ the 5'-phosphate and the 3'-hydroxyl. The keyword \"phosphoprotein\" is not\
\ used with polynucleotide-linked intermediate modifications. Generating Enzyme:\
\ formamidopyrimidine-DNA glycosylase (EC 3.2.2.23)."
synonyms:
- (1Z,2S)-2-carboxy-1-[(3R,4R)-3,4-dihydroxy-5-(phosphonooxy)pentylidene]pyrrolidinium
- DNA glycosylase proline Schiff base intermediate [misnomer]
identifiers:
- ns: resid
id: AA0494
- ns: mod
id: MOD:01454
- ns: pdb.ligand
id: PED
structure: OP(OC[C@H]([C@H](CC[NH+]1CCC[C@H]1C(=O)O)O)O)O
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
- molecule: Monomer
element: H
position: 20
AA0067:
id: AA0067
name: omega-N,omega-N'-dimethyl-L-arginine
comments: 'This modification should not be confused with omega-N,omega-N-dimethyl-L-arginine
(see RESID:AA0068) or N2,N2-dimethyl-L-arginine (see RESID:AA0569). Generating
Enzyme: [myelin basic protein]-arginine N-methyltransferase (EC 2.1.1.126).'
synonyms:
- (2S)-2-amino-5-[((methylamino)(methylimino)methyl)amino]pentanoic acid
- N5-[(methylamino)(methylimino)methyl]ornithine
- NG,N'G-dimethylarginine
- symmetric dimethylarginine
- (2S)-2-amino-5-[(N,N'-dimethylcarbamimidoyl)amino]pentanoic acid
- n3, n4-dimethylarginine
- N~5~-(N,N'-dimethylcarbamimidoyl)-L-ornithine
- N3,N4-dimethylarginine
- R
identifiers:
- ns: pdb.ligand
id: 2MR
- ns: cas
id: 30344-00-4
- ns: pdb-ccd
id: 2MR
- ns: go
id: GO:0018216
- ns: mod
id: MOD:00076
- ns: chebi
id: CHEBI:61916
- ns: resid
id: AA0067
structure: CNC(NCCC[C@@H](C(=O)O)[NH3+])NC
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
AA0120:
id: AA0120
name: N6-retinylidene-L-lysine
comments: The all-trans form is shown. Light-induced interconversion with the
11-cis (4Z) form in rhodopsin is the basis for light sensing in animals. Light-induced
interconversion with the 13-cis (2Z) form in bacteriorhodopsin is utilized for
proton pumping in some archaea.
synonyms:
- n~6~-[(2z,4e,6e,8e)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenyl]lysine
- (2S)-2-amino-6-[[(2E,4Z,6E)-3,7-dimethyl-9-(2,6,6-trimethyl-1-cyclohexenyl)nona-2,4,6,8-tetraenyl]amino]hexanoic
acid
- N6-retinyl-lysine
- K
- N6-retinal-L-lysine
- N~6~-[(2E,4Z,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraen-1-yl]-L-lysine
- (2S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic
acid
identifiers:
- ns: pdb.ligand
id: LYR
- ns: resid
id: AA0120
- ns: mod
id: MOD:00129
- ns: pdb-ccd
id: LYR
- ns: go
id: GO:0018273
- ns: cas
id: 116-31-4
structure: C[C@@H](/C=C/C=C(/C=C/C1=C(C)CCCC1(C)C)\C)/C=C/[NH2+]CCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 31
l_bond_atoms:
- molecule: Monomer
element: N
position: 34
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 33
- molecule: Monomer
element: H
position: 33
l_displaced_atoms:
- molecule: Monomer
element: H
position: 34
- molecule: Monomer
element: H
position: 34
charge: 1
AA0274:
id: AA0274
name: N-pyruvic acid 2-iminyl-L-cysteine
comments: The cysteine sulfhydryl may cyclize with the imine to form 2-methyl-thiazolidine-2,4-dicarboxylic
acid [CAS:152574-58-8].
synonyms:
- (R)-2-(1-carboxy-2-sulfanylethanimino)propanoic acid
identifiers:
- ns: resid
id: AA0274
- ns: mod
id: MOD:00279
- ns: go
id: GO:0018386
structure: SC[C@H]([NH2+][C@H](C(=O)[O-])C)C=O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
AA0058:
id: AA0058
name: N-D-glucuronyl-glycine
comments: The glucuronic acid is linked as an amide, rather than as a glycoside
(see RESID:AA0291). The alpha glucuronoyl form is shown.
synonyms:
- 2-(glucuronoylamino)ethanoic acid
- N-D-glucuronyl-glycine
identifiers:
- ns: mod
id: MOD:00067
- ns: cas
id: 62532-50-7
- ns: go
id: GO:0018007
- ns: resid
id: AA0058
structure: OC(=O)CNC(=O)[C@H]1O[C@@H](O)[C@@H]([C@H]([C@@H]1O)O)O
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
C, H:
id: AA0436
name: 6-(S-L-cysteinyl)-8alpha-(-3'-L-histidino)-FAD
comments: 'The keyword "phosphoprotein" is not used with flavin modifications
linked through the flavin. Generating Enzyme: autocatalytic.'
synonyms:
- 6-(S-cysteinyl)-8alpha-(N(delta1)-histidyl)-FAD
- 6-(S-cysteinyl)-8alpha-(N3'-histidyl)-FAD
- 6-(S-cysteinyl)-8alpha-(N(pi)-histidyl)-FAD
- 6-((R)-2-amino-2-carboxyethyl)sulfanyl-8alpha-[4-((S)-2-amino-2-carboxyethyl)imidazol-3-yl]-riboflavin
5'-(trihydrogen diphosphate) 5'->5'-ester with adenosine
- 6-(S-cysteinyl)-8alpha-(pros-histidyl)-FAD
identifiers:
- ns: pdb.ligand
id: FAD
- ns: mod
id: MOD:01182
- ns: resid
id: AA0436
structure: O=C[C@H](CSC1=C(C)[C@@H](C=C2C1=N[C@H]1C(=O)NC(=O)N=C1N2C[C@@H]([C@@H]([C@@H](CO[P@](=O)(O[P@@](=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1NC=N[C@@H]2N)[O-])[O-])O)O)O)Cn1cncc1C[C@@H](C(=O)O)[NH3+])[NH3+]
base_monomers:
- C
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 78
l_bond_atoms:
- molecule: Monomer
element: N
position: 81
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 80
- molecule: Monomer
element: H
position: 80
l_displaced_atoms:
- molecule: Monomer
element: H
position: 81
- molecule: Monomer
element: H
position: 81
charge: 1
AA0075:
id: AA0075
name: N6,N6-dimethyl-L-lysine
comments: 'This modification is readily formed artifactually by reductive methylation
using formaldehyde. Generating Enzyme: histone-lysine N-methyltransferase (EC
2.1.1.43); cytochrome-c-lysine N-methyltransferase (EC 2.1.1.59); calmodulin-lysine
N-methyltransferase (EC 2.1.1.60).'
synonyms:
- n-dimethyl-lysine
- (2S)-2-amino-6-dimethylamino-hexanoic acid
- N~6~,N~6~-dimethyl-L-lysine
- epsilon-dimethyllysine
- lysine derivative Lys(y)
- K
- N(zeta)-dimethyllysine
- (2S)-2-amino-6-(dimethylamino)hexanoic acid
identifiers:
- ns: chebi
id: CHEBI:61969
- ns: resid
id: AA0075
- ns: go
id: GO:0018024
- ns: cas
id: 2259-86-1
- ns: pdb.ligand
id: MLY
- ns: pdb-ccd
id: MLY
- ns: mod
id: MOD:00084
structure: C[NH+](CCCC[C@@H](C(=O)O)[NH3+])C
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
M, Y:
id: AA0377
name: 3-(2-methylthio)ethyl-6-(4-hydroxybenzylidene)-5-iminopiperazin-2-one
comments: The correct structure for the asFP595 chromophore is now thought to
be a para-hydroxybenzylidene-5-imidazolidinone. See RESID:AA0379. The diagram
presents structures for two tautomeric forms with the glycine, which is linked
by either an imino or amino group, shown in gray. In the correct structure,
the glycine amino group forms part of a 5-member ring.
synonyms:
- 3-(2-methylthio)ethyl-6-(4-hydroxybenzylidene)-5-amino-3,6-didehydropyrazin-2-ol
- GFP-like chromoprotein asFP595 chromophore
- L-methionyl-L-tyrosyl-2-keto-5-iminopiperazine
- 3-(2-methylsulfanyl)ethyl-6-(4-hydroxybenzylidene)-5-iminopiperazin-2-one
identifiers:
- ns: resid
id: AA0377
- ns: go
id: GO:0051357
- ns: mod
id: MOD:00382
structure: CSCC[C@@H]1N[C@@H](NCC(=O)O)/C(=C\c2ccc(cc2)O)/NC1=O
base_monomers:
- M
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
AA0307:
id: AA0307
name: S-myristoyl-L-cysteine
comments: 'The predominant palmitoyl transferase in mammalian systems appears
to utilize a mixture of saturated and unsaturated fatty acids including myristoic
acid. Some systems may be more specific in their incorporation of other fatty
acids. See RESID:AA0106 and RESID:AA0308. Generating Enzyme: protein-cysteine
S-myristoyltransferase (EC 2.3.1.-).'
synonyms:
- tetradecanoate cysteine thioester
- (R)-2-amino-3-(tetradecanoylsulfanyl)propanoic acid
identifiers:
- ns: chebi
id: CHEBI:22061
- ns: pdb.ligand
id: MYR
- ns: mod
id: MOD:00312
- ns: resid
id: AA0307
- ns: go
id: GO:0019704
structure: CCCCCCCCCCCCCC(=O)SC[C@@H](C(=O)O)N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 23
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: H
position: 23
AA0591:
id: AA0591
name: N-palmitoyl-L-methionine
comments: 'Generating Enzyme: methionylpeptide N-palmitoyltransferase (EC 2.3.1.-).'
synonyms:
- N-(1-oxohexadecyl)methionine
- 2-(hexadecanamido)-4-(methylsulfanyl)butanoic acid
- (2S)-2-(hexadecanoylamino)-4-(methylsulfanyl)butanoic acid
identifiers:
- ns: mod
id: MOD:01937
- ns: cas
id: 36416-81-6
- ns: resid
id: AA0591
structure: CCCCCCCCCCCCCCCC(=O)N[C@H](C(=O)O)CCSC
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 21
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
r_displaced_atoms:
- molecule: Monomer
element: O
position: 23
- molecule: Monomer
element: H
position: 23
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
AA0098:
id: AA0098
name: L-tryptophan amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- (2S)-2-amino-3-(1H-indol-3-yl)propanamide
- tryptophanamide
identifiers:
- ns: mod
id: MOD:00107
- ns: cas
id: 20696-57-5
- ns: go
id: GO:0018051
- ns: resid
id: AA0098
- ns: chebi
id: CHEBI:16533
- ns: pdb.ligand
id: NH2
structure: NC(=O)[C@H](Cc1c[nH]c2c1cccc2)[NH3+]
base_monomers:
- W
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0190:
id: AA0190
name: D-aspartic acid
comments: The stereoisomeric conversion of L-aspartic acid or L-asparagine to
D-aspartic acid is probably mediated by the spontaneous cyclization and deamidation
to a 2-aminosuccinimidyl group (see RESID:AA0441).
synonyms:
- (2R)-2-aminobutanedioic acid
- aminosuccinic acid
- 2-azanylbutanedioic acid
identifiers:
- ns: pdb.ligand
id: DAS
- ns: resid
id: AA0190
- ns: mod
id: MOD:01921
- ns: cas
id: 1783-96-6
- ns: chebi
id: CHEBI:48094
- ns: mod
id: MOD:01930
structure: O=C[C@@H](CC(=O)[O-])[NH3+]
base_monomers:
- N
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
AA0193:
id: AA0193
name: D-methionine
comments: 'Generating Enzyme: protein-methionine epimerase (EC 5.1.1.-).'
synonyms:
- 2-amino-4-(methylthio)butyric acid
- (2R)-2-amino-4-(methylsulfanyl)butanoic acid
- 2-amino-4-(methylthio)butanoic acid
identifiers:
- ns: chebi
id: CHEBI:29984
- ns: pdb.ligand
id: MED
- ns: resid
id: AA0193
- ns: go
id: GO:0019123
- ns: cas
id: 348-67-4
- ns: mod
id: MOD:00200
structure: CSCC[C@@H]([NH3+])C(=O)O
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
AA0354:
id: AA0354
name: N2-acetyl-L-arginine
comments: 'The common peptide alpha-N-acetyltransferase does not acetylate basic
residues, so another alpha-acetyltransferase activity must be producing this
modification in a thylakoid protein. Generating Enzyme: arginylpeptide alpha-N-acetyltransferase
(EC 2.3.1.-).'
synonyms:
- acetylarginine
- 2-acetylamino-5-guanidinopentanoic acid
- (S)-2-acetamido-5-carbamimidamidopentanoic acid
- 2-acetamido-5-guanidinopentanoic acid
- N(alpha)-acetylarginine
- alpha-acetylamino-delta-guanidinovaleric acid
identifiers:
- ns: resid
id: AA0354
- ns: mod
id: MOD:00359
- ns: cas
id: 155-84-0
- ns: go
id: GO:0048275
structure: CC(=O)N[C@H](C(=O)O)CCC[NH+]=C(N)N
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
C, C:
id: AA0429
name: 15,16-dihydrobiliverdin-bis-L-cysteine
comments: This bilin transmits violet. The stereochemistry for the 18' chiral
center has not been resolved.
synonyms:
- (16R)-8,12-bis(2-carboxyethyl)-3-[2-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-18-[(1Xi)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-2,7,13,17-tetramethyl-15,16-dihydrobilin-1,19(21H,24H)-dione
- 3'',18'-biscysteinyl-15,16-dihydrobiliverdin
- 15,16-dihydrobiliverdin cysteine adduct
- 3beta,18alpha-biscysteinyl-15,16-dihydrobiliverdin
- 8,12-bis(2-carboxyethyl)-3-(2-(cysteinyl-S)-ethyl)-18-(1-(cysteinyl-S)-ethyl)-2,7,13,17-tetramethylbiladiene-ab-1,19(16H,21H)-dione
- DBV
- 15,16-dihydrobiliverdin IXalpha
- 15,16-Dhbv
identifiers:
- ns: cas
id: 137429-14-2
- ns: resid
id: AA0429
- ns: pdb.ligand
id: DBV
- ns: mod
id: MOD:01143
structure: O=C[C@H](CSCCC1=C(C)C(=O)N/C/1=C\c1[nH]c(c(c1C)CCC(=O)[O-])Cc1[nH]c(c(c1CCC(=O)[O-])C)C[C@H]1NC(=O)C(=C1C)[C@@H](SC[C@@H](C=O)[NH3+])C)[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 26
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
r_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
T, T:
id: AA0572
name: L-threonine 5-methyloxazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-threonine
cyclase (EC 4.2.1.-); peptidyl-oxazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-[(1S,2R)-1-amino-2-hydroxypropyl]-5-methyl-1,3-oxazole-4-carboxylic acid
- 2-[(1S,2R)-1-azanyl-2-hydroxypropyl]-5-methyl-1,3-oxazole-4-carboxylic acid
identifiers:
- ns: mod
id: MOD:01901
- ns: resid
id: AA0572
structure: C[C@H]([C@@H](c1oc(c(n1)C(=O)O)C)N)O
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
AA0388:
id: AA0388
name: 4-hydroxy-D-valine
synonyms:
- (2R,3Xi)-2-amino-4-hydroxy-3-methylbutanoic acid
- D-gamma-hydroxyvaline
identifiers:
- ns: resid
id: AA0388
- ns: mod
id: MOD:00756
structure: OC[C@H]([C@H](C(=O)O)[NH3+])C
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
AA0278:
id: AA0278
name: N6-propylamino-poly(propylmethylamino)-propyldimethylamine-L-lysine
comments: In silaffin from the diatom Cylindrotheca fusiformis there are five
to eleven N-methyl-propylamine monomeric units on each lysine. Six are shown.
synonyms:
- lysine derivative Lys(x)
- N6-[3-([(omega)-(dimethyl)aminopropyl-poly(3-[methylamino]propyl)]amino)propyl]lysine
- (alpha)- ([([(5S)-5-amino-5-carboxypentyl]amino)propyl][(methyl)amino])-(omega)-methyl
poly[propane-1,3-diyl(methylimino)]
- silaffin polycationic lysine derivative
identifiers:
- ns: go
id: GO:0018185
- ns: mod
id: MOD:00283
- ns: resid
id: AA0278
structure: C[NH+](CCCNCCC[NH2+]CCCC[C@@H](C(=O)O)[NH3+])CCCN(CCC[NH+](CCCN(CCC[NH+](C)C)C)C)C
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 23
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: H
position: 23
- molecule: Monomer
element: H
position: 23
charge: 1
AA0117:
id: AA0117
name: N6-biotinyl-L-lysine
comments: 'Generating Enzyme: biotin--protein ligase (EC 6.3.4.-); biotin--[methylmalonyl-CoA-carboxyltransferase]
ligase (EC 6.3.4.9); biotin--[propionyl-CoA-carboxylase (ATP-hydrolysing)] ligase
(EC 6.3.4.10); biotin--[methylcrotonoyl-CoA-carboxylase] ligase (EC 6.3.4.11);
biotin--[acetyl-CoA-carboxylase] ligase (EC 6.3.4.15).'
synonyms:
- N6-biotinyllysine
- epsilon-N-biotinyllysine
- (2S)-2-amino-6-(5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoylamino)hexanoic
acid
- biocytin
- (3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine
- N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine
identifiers:
- ns: resid
id: AA0117
- ns: cas
id: 576-19-2
- ns: go
id: GO:0018054
- ns: mod
id: MOD:00126
- ns: pdb.ligand
id: BTN
structure: O=C(NCCCC[C@@H](C(=O)O)[NH3+])CCCC[C@@H]1SC[C@H]2[C@@H]1NC(=O)N2
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
AA0576:
id: AA0576
name: N-formyl-L-alanine
synonyms:
- (2S)-2-(formylamino)propanoic acid
- 2-formamidopropionic acid
- 2-formamidopropanoic acid
identifiers:
- ns: cas
id: 10512-86-4
- ns: resid
id: AA0576
- ns: pdb.ligand
id: FOR
- ns: mod
id: MOD:01915
structure: O=CN[C@H](C(=O)O)C
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 3
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
- molecule: Monomer
element: H
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 3
AA0602:
id: AA0602
name: (2R)-2-hydroxyproline
comments: 'The chemical stability of this modification has been questioned. However,
a similar modification in an homologous enzyme has apparently been observed
by another group in work that has not yet been published. Generating Enzyme:
autocatalytic.'
synonyms:
- alpha-hydroxyproline
- (2R)-2-oxidanylpyrrolidine-2-carboxylic acid
- 2-hydroxy-L-proline
- 2-hydroxy-l-proline
- (2R)-2-hydroxypyrrolidine-2-carboxylic acid
- 2-oxidanylpyrrolidine-2-carboxylic acid
identifiers:
- ns: resid
id: AA0602
- ns: pdb-ccd
id: PXU
- ns: pdb.ligand
id: PXU
- ns: mod
id: MOD:01957
structure: OC(=O)[C@]1(O)CCC[NH2+]1
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
C, N:
id: AA0469
name: L-asparagine 5-methylthiazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-cysteine
cyclase (EC 4.2.1.-); peptidyl-thiazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-[(1S)-1,3-diamino-3-oxopropyl]-5-methyl-1,3-thiazole-4-carboxylic acid
- 2-[(1S)-1,3-bisazanyl-3-oxopropyl]-5-methyl-1,3-thiazole-4-carboxylic acid
identifiers:
- ns: mod
id: MOD:01392
- ns: resid
id: AA0469
structure: NC(=O)C[C@@H](c1nc(c(s1)C)C(=O)O)N
base_monomers:
- N
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
AA0308:
id: AA0308
name: S-palmitoleyl-L-cysteine
comments: 'This specific modification has been detected but not located by sequencing
in proteins. This modification may also arise from non-specific activity of
the enzymes that produce S-palmitoyl-L-cysteine; see RESID:AA0106. Generating
Enzyme: protein-cysteine S-palmitoleyltransferase (EC 2.3.1.-).'
synonyms:
- cis-9-hexadecenoate cysteine thioester
- (R)-2-amino-3-((Z)-9-hexadecenoylsulfanyl)propanoic acid
identifiers:
- ns: mod
id: MOD:00313
- ns: go
id: GO:0019939
- ns: resid
id: AA0308
structure: CCCCCC/C=C\CCCCCCCC(=O)SC[C@@H](C(=O)O)N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 22
l_bond_atoms:
- molecule: Monomer
element: N
position: 25
r_displaced_atoms:
- molecule: Monomer
element: O
position: 24
- molecule: Monomer
element: H
position: 24
l_displaced_atoms:
- molecule: Monomer
element: H
position: 25
AA0176:
id: AA0176
name: L-4'-bromophenylalanine
synonyms:
- 4-bromo-l-phenylalanine
- p-bromophenylalanine
- 4-bromo-L-phenylalanine
- (2S)-2-amino-3-(4-bromophenyl)propanoic acid
- para-bromophenylalanine
- Y
identifiers:
- ns: pdb.ligand
id: 4BF
- ns: mod
id: MOD:00185
- ns: resid
id: AA0176
- ns: cas
id: 24250-84-8
- ns: go
id: GO:0018075
- ns: pdb-ccd
id: 4BF
structure: '[NH3+][C@H](C(=O)O)Cc1ccc(cc1)Br'
base_monomers:
- F
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
A, G:
id: AA0187
name: L-alanine 5-imidazolinone glycine
comments: This entry represents the cross-link of the peptide backbone from the
alpha-carboxyl carbon of residue N, an alanine, to the alpha-amino nitrogen
of residue N+2, a glycine, coupled with the formation of a double bond to the
alpha-amino nitrogen of residue N+1 which loses one hydrogen, and the loss of
a molecule of water. This cross-link is accompanied by modification of residue
N+1. The modified residue N+1 is presented in a separate entry and is not included
in the mass accounting of this entry. The backbone atoms of residue N+1 are
shown in gray in the diagram.
synonyms:
- 4-methylidene-imidazole-5-one active site
- alanyl-5-imidazolinone glycine
- 2-[1-aminoethyl]-1-carboxymethyl-1-imidazolin-5-one
- (2-[(1S)-1-aminoethyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl)acetic acid
- para-hydroxybenzylidene-imidazolidinone chromophore
identifiers:
- ns: mod
id: MOD:00195
- ns: pdb.ligand
id: AYG
- ns: resid
id: AA0187
- ns: go
id: GO:0018253
structure: OC(=O)CN1C(=O)CN=C1[C@@H]([NH3+])C
base_monomers:
- A
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
AA0479:
id: AA0479
name: (2S,3R,4R)-3,4-dihydroxyproline
synonyms:
- 2-alpha-3-beta-4-alpha-3,4-dihydroxyproline
- (2S,3R,4R)-3,4-dihydroxypyrrolidine-2-carboxylic acid
- 2,3-trans-3,4-trans-3,4-dihydroxy-L-proline
identifiers:
- ns: resid
id: AA0479
- ns: cas
id: 74644-88-5
- ns: mod
id: MOD:01402
structure: O[C@@H]1C[NH2+][C@@H]([C@H]1O)C(=O)O
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
AA0129:
id: AA0129
name: 2-oxobutanoic acid
synonyms:
- 2-ketobutyric acid
- 2-oxobutanoic acid
- 2-oxobutyric acid
identifiers:
- ns: chebi
id: CHEBI:30831
- ns: pdb.ligand
id: 2KT
- ns: cas
id: 600-18-0
- ns: resid
id: AA0129
- ns: go
id: GO:0018058
- ns: mod
id: MOD:00138
structure: CCC(=O)C(=O)O
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
- molecule: Monomer
element: H
position: 7
AA0487:
id: AA0487
name: 4-hydroxy-L-glutamic acid
comments: This modification is currently represented in the PDB as part of the
HET group for the entire molecule of nosiheptide. The chirality of C-4 is not
settled. The (2S,4S) diastereomer is shown.
synonyms:
- (2S,4Xi)-2-amino-4-hydroxypentanedioic acid
- gamma-hydroxy glutaminic acid
- (2s,4s)-2-amino-4-hydroxy-pentanedioic acid
- threo-4-hydroxy-L-glutamic acid
- (2S,4S)-2-amino-4-hydroxy-pentanedioic acid
- (2S,4S)-2-amino-4-hydroxypentanedioic acid (non-preferred name)
identifiers:
- ns: cas
id: 3913-68-6
- ns: pdb-ccd
id: 3GL
- ns: mod
id: MOD:01434
- ns: resid
id: AA0487
- ns: pdb.ligand
id: 3GL
structure: O=C[C@H](C[C@@H](C(=O)[O-])O)[NH3+]
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
AA0104:
id: AA0104
name: S-geranylgeranyl-L-cysteine
comments: 'For the type I geranylgeranyltransferase the residue may be found at
the first position in the sequence motif CXX[LF]* where the second and third
positions are usually aliphatic. For the type II geranylgeranyltransferase the
residue may be found at the first and final positions in the sequence motif
CXC* or at the final two positions in the sequence motif CC*. These motifs are
necessary but not sufficient for modification. Formation of S-geranylgeranylcysteine
may be coupled with subsequent cleavage of a carboxy-terminal tripeptide for
the CAAX motif and methyl esterification of the geranylgeranylated cysteine.
Methyl esterification without cleavage occurs for the CXC motif. Generating
Enzyme: protein-cysteine geranylgeranyltransferase (EC 2.5.1.-).'
synonyms:
- (2R)-2-amino-3-([(2E,6E,10Z)-12-hydroxy-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]sulfanyl)propanoic
acid
- 2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid
identifiers:
- ns: go
id: GO:0018228
- ns: cas
id: 131404-69-8
- ns: pdb.ligand
id: GER
- ns: resid
id: AA0104
- ns: mod
id: MOD:00113
structure: C/C(=C\CC/C(=C/CSC[C@@H](C(=O)O)[NH3+])/C)/CC/C=C(/CCC=C(C)C)\C
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0258:
id: AA0258
name: S-phycobiliviolin-L-cysteine
comments: The phycoviolobilins transmit violet. It has not been established whether
the chromophores that have been referred to as cryptoviolins have the same structure
as phycoviolobilin.
synonyms:
- (4S)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-18-ethyl-4,5-dihydro-2,7,13,17-tetramethyl-(21H,22H,24H)-biladiene-bc-1,19-dione
- PVB
- PBV
- S-phycobiliviolin-L-cysteine
- cryptoviolin
- cryptoviolobilin
- PXB
- cryptobiliviolin
identifiers:
- ns: pdb.ligand
id: PVN
- ns: go
id: GO:0017008
- ns: mod
id: MOD:00263
- ns: resid
id: AA0258
- ns: cas
id: 124861-40-1
structure: O=C[C@H](CS[C@@H](C1=C(C)C(=O)N[C@H]1Cc1[nH]c(c(c1C)CCC(=O)[O-])Cc1[nH]c(c(c1CCC(=O)[O-])C)/C=C\1/NC(=O)C(=C1C)CC)C)[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 27
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
r_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
O:
id: AA0321
name: N6-(4-methyl-delta-1-pyrroline-5-carboxyl)-L-lysine
comments: 'Pyrrolysine is encoded by the UAG codon in some genetic systems. Although
the single letter symbol O is recommended by IUBMB, most software applications
fail to recognize it, and many sequence databases use the single letter symbol
K. Proposed enzyme names are presented. There is evidence for the third reaction
with an ornithine substrate, but not yet for the 3-methylornithine substrate,
and the redox cofactor has not been identified. Generating Enzyme: lysine--tRNA(Pyl)
ligase (EC 6.1.1.25); pyrrolysine--tRNA(Pyl) ligase (EC 6.1.1.26); (3R)-3methyl-D-ornithine
carboxy-aminomethylmutase, PylB (EC 5.4.99.-); (3R)-3-methyl-D-ornithine--L-lysine
ligase, PylC (EC 6.3.2.-); N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine N5-ornithine
dehydrogenase, PylD (EC 1.4.1.-).'
synonyms:
- N6-([(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl)-L-lysine
- monomethylamine methyltransferase cofactor lysine adduct
- N6-(4-methyl-delta-1-pyrroline-5-carboxyl)-L-lysine
- N6-(4-methyl-1,2-didehydropyrrolidine-5-carboxyl)-L-lysine
- (2S)-2-amino-6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]aminohexanoic
acid
- 2-azanyl-6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]azanylhexanoic
acid
identifiers:
- ns: resid
id: AA0321
- ns: mod
id: MOD:00326
- ns: go
id: GO:0030631
- ns: pdb.ligand
id: BGX
- ns: cas
id: 448235-52-7
- ns: mod
id: MOD:01187
- ns: chebi
id: CHEBI:21860
structure: OC(=O)[C@H](CCCCNC(=O)[C@@H]1[NH2+]CC[C@H]1C)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 23
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 23
- molecule: Monomer
element: H
position: 23
charge: 1
I, S:
id: AA0573
name: L-isoleucine oxazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-serine
cyclase (EC 4.2.1.-); peptidyl-oxazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-[(1S,2S)-1-azanyl-2-methylbutyl]-1,3-oxazole-4-carboxylic acid
- 2-[(1S,2S)-1-amino-2-methylbutyl]-1,3-oxazole-4-carboxylic acid
identifiers:
- ns: resid
id: AA0573
- ns: mod
id: MOD:01902
structure: C[C@H]([C@H]([NH3+])c1nc(co1)C(=O)O)CC
base_monomers:
- I
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
- molecule: Monomer
element: H
position: 17
C, T:
id: AA0485
name: L-threonine thiazoline-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue. The ring may be oxidized to thiazole and then reduced
from the opposite side effectively inverting the cysteine alpha-carbon chirality.
Generating Enzyme: peptidyl-cysteine cyclase (EC 4.2.1.-).'
synonyms:
- (4S)-2-[(1S,2R)-1-amino-2-hydroxypropyl]-4,5-dihydro-1,3-thiazole-4-carboxylic
acid
- 2-[1-azanyl-2-hydroxypropyl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid
identifiers:
- ns: mod
id: MOD:01408
- ns: pdb.ligand
id: BB9
- ns: resid
id: AA0485
structure: C[C@H]([C@@H]([C@H]1SC[C@H](N1)C(=O)O)[NH3+])O
base_monomers:
- T
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
AA0497:
id: AA0497
name: O-(2-aminoethylphosphoryl)-L-serine
synonyms:
- serine ethanolamine phosphate
- O3-(phosphoethanolamine)-L-serine
- O3-(2-aminoethylphosphoryl)-L-serine
- serine ethanolamine phosphodiester
- (2S)-2-amino-3-([(2-aminoethoxy)(hydroxy)phosphoryl]oxy)propanoic acid
identifiers:
- ns: pdb.ligand
id: OPE
- ns: resid
id: AA0497
- ns: cas
id: 1186-34-1
- ns: mod
id: MOD:01587
structure: '[O-]P(=O)(OCC[NH3+])OC[C@H]([NH3+])C(=O)O'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 19
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 21
- molecule: Monomer
element: H
position: 21
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0099:
id: AA0099
name: L-tyrosine amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- (2S)-2-amino-3-(4-hydoxyphenyl)propanamide
- tyrosinamide
identifiers:
- ns: mod
id: MOD:00108
- ns: resid
id: AA0099
- ns: cas
id: 4985-46-0
- ns: chebi
id: CHEBI:21412
- ns: go
id: GO:0018052
- ns: pdb.ligand
id: NH2
structure: '[NH3+][C@H](C(=O)N)Cc1ccc(cc1)O'
base_monomers:
- Y
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
G, S:
id: AA0184
name: L-serine 5-imidazolinone glycine
comments: 'This entry represents the cross-link of the peptide backbone from the
alpha-carboxyl carbon of residue N, a serine, to the alpha-amino nitrogen of
residue N+2, a glycine, coupled with the formation of a double bond to the alpha-amino
nitrogen of residue N+1 which loses one hydrogen, and the loss of a molecule
of water. This cross-link is accompanied by modification of residue N+1. The
modified residue N+1 is presented in a separate entry and is not included in
the mass accounting of this entry. The backbone atoms of residue N+1 are shown
in gray in the diagram. The chirality of residue N is (R) rather then (S) because
of the reversed order of precedence with respect to the beta-carbon methoxy
group of the 5-imidazolinone group replacing the carboxyl group. The modification
of serine to dehydroalanine coupled with the formation of 5-imidazolinone by
the two neighboring residues produces the 4-methylidene-imidazole-5-one (MIO)
active site of some amino acid ammonia-lyases that differs by UV and mass spectrometric
evidence from other known dehydroalanine containing peptides not containing
the second modification. Generating Enzyme: autocatalytic.'
synonyms:
- '[(4z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic
acid'
- seryl-5-imidazolinone glycine
- '[(4Z)-2-[(1R)-1-amino-2-hydroxyethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic
acid'
- green fluorescent protein chromophore
- para-hydroxybenzylidene-imidazolidinone chromophore
- 2-[(4Z)-2-[(1R)-1-azanyl-2-oxidanyl-ethyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
- 4-methylidene-imidazole-5-one (MIO) active site
- 2-[1-amino-2-hydroxyethyl]-1-carboxymethyl-1-imidazolin-5-one
- (2-[(1R)-1-amino-2-hydroxyethyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl)acetic acid
- SYG
identifiers:
- ns: pdb.ligand
id: GYS
- ns: resid
id: AA0184
- ns: mod
id: MOD:00192
- ns: go
id: GO:0018252
- ns: pdb-ccd
id: GYS
structure: OC[C@@H](C1=NCC(=O)N1CC(=O)O)[NH3+]
base_monomers:
- S
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
C, E:
id: AA0488
name: 2-(cystein-S-ylcarbonyl)-3-methyl-4-(glutam-5-yloxy)methylindole
comments: This modification is currently represented in the PDB as part of the
HET group for the entire molecule of nosiheptide.
synonyms:
- 2-([(1R)-1-amino-1-carboxyeth-2-yl]sulfanyl)carbonyl-3-methyl-4-([(1S)-1-amino-1-carboxy-4-oxobutan-4-yl]oxy)methyl-1H-indole
- 2-(cystein-S-ylcarbonyl)-4-[(glutam-5-yloxy)methyl]-3-methyl-1H-indole
identifiers:
- ns: pdb.ligand
id: NO1
- ns: mod
id: MOD:01435
- ns: resid
id: AA0488
structure: O=C[C@H](CCC(=O)OCc1cccc2c1c(C)c([nH]2)C(=O)SC[C@@H](C(=O)O)N)[NH3+]
base_monomers:
- E
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 28
l_bond_atoms:
- molecule: Monomer
element: N
position: 31
r_displaced_atoms:
- molecule: Monomer
element: O
position: 30
- molecule: Monomer
element: H
position: 30
l_displaced_atoms:
- molecule: Monomer
element: H
position: 31
AA0409:
id: AA0409
name: L-2-aminobutanoic acid
comments: 'Exposure of green fluorescent protein to 254 nm UV light or to 390
nm visible light causes gamma decarboxylation of glutamic acid 222. Unlike the
threonine in 3-methylanthionine, the L configuration (S chirality) of the 2-aminobutanoate
skeleton is maintained. Generating Enzyme: autocatalytic.'
synonyms:
- (S)-2-aminobutanoic acid
- L-alpha-amino-n-butyric acid
- L-alpha-aminobutyric acid
- L-2-amino-n-butyric acid
- L-butyrine
- L-2-aminobutyric acid
identifiers:
- ns: chebi
id: CHEBI:35619
- ns: cas
id: 1492-24-6
- ns: pdb.ligand
id: ABA
- ns: mod
id: MOD:00819
- ns: resid
id: AA0409
structure: CC[C@H]([NH3+])C(=O)O
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
- molecule: Monomer
element: H
position: 11
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
AA0180:
id: AA0180
name: 6'-chloro-L-tryptophan
synonyms:
- W
- 6-chloro-L-tryptophan
- (2S)-2-amino-3-(6-chloro-1H-indol-3-yl)propanoic acid
- 6-chloro-l-tryptophan
identifiers:
- ns: cas
id: 17808-35-4
- ns: pdb.ligand
id: 6CW
- ns: mod
id: MOD:00886
- ns: pdb-ccd
id: 6CW
- ns: resid
id: AA0180
structure: OC(=O)[C@H](Cc1c[nH]c2c1ccc(c2)Cl)[NH3+]
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0045:
id: AA0045
name: N-acetyl-L-glutamine
comments: The occurrence of this modification has not been confirmed. Formerly,
its annotation in sequence databases was due to either the misidentification
of 2-pyrrolidone-5-carboxylic acid, or inappropriate homolog comparisons when
proteolytic modification was more probable.
synonyms:
- 2-acetylamino-5-pentanediamic acid
- 2-acetylamino-5-amino-5-oxopentanoic acid
- (2S)-2-acetamido-5-pentanediamic acid
- acetylglutamine
- 2-acetylazanyl-5-azanyl-5-oxopentanoic acid
identifiers:
- ns: chebi
id: CHEBI:21553
- ns: resid
id: AA0045
- ns: cas
id: 2490-97-3
- ns: go
id: GO:0017192
- ns: mod
id: MOD:00054
structure: NC(=O)CC[C@@H](C(=O)O)NC(=O)C
base_monomers:
- Q
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
AA0448:
id: AA0448
name: (3R,4S)-4-hydroxyisoleucine
comments: In peptide sequencing work prior to 1968, this modification was reported
as a beta-methylleucine derivative that could arise by either beta-methylation
of leucine or gamma-methylation of isoleucine. The correct structure has been
determined to be derived from isoleucine without methylation.
synonyms:
- gamma-hydroxyisoleucine
- (2S,3R,4S)-2-amino-3-methyl-4-hydroxyvaleric acid
- (3R,4S)-4-hydroxyisoleucine
- (2S,3R,4S)-2-amino-4-hydroxy-3-methylpentanoic acid
identifiers:
- ns: resid
id: AA0448
- ns: mod
id: MOD:01377
structure: C[C@@H]([C@@H]([C@@H](C(=O)O)[NH3+])C)O
base_monomers:
- I
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
AA0174:
id: AA0174
name: L-2'-bromophenylalanine
synonyms:
- (S)-2-amino-3-(2-bromophenyl)propanoic acid
- ortho-bromophenylalanine
- o-bromophenylalanine
identifiers:
- ns: cas
id: 42538-40-9
- ns: mod
id: MOD:00183
- ns: resid
id: AA0174
- ns: go
id: GO:0018075
structure: OC(=O)[C@H](Cc1ccccc1Br)[NH3+]
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
AA0147:
id: AA0147
name: L-2',4',5'-topaquinone
synonyms:
- 2,4,5-trihydroxyphenylalanine quinone
- (2S)-2-amino-3-(4-hydroxy-3,6-dioxo-1-cyclohexa-1,4-dienyl)propanoic acid
- 5-(2-carboxy-2-aminoethyl)-2-hydroxy-1,4-benzoquinone
- TPQ
- (2S)-2-amino-3-(5-hydroxy-2,5-cyclohexadien-1,4-dion-2-yl)propanoic acid
- Y
- L-2,4,5-TOPAquinone
- 3-(4-hydroxy-3,6-dioxocyclohexa-1,4-dien-1-yl)-L-alanine
identifiers:
- ns: pdb.ligand
id: TPQ
- ns: resid
id: AA0147
- ns: chebi
id: CHEBI:21187
- ns: pdb-ccd
id: TPQ
- ns: go
id: GO:0018068
- ns: mod
id: MOD:00156
structure: '[O-]C1=CC(=O)C(=CC1=O)C[C@H]([NH3+])C(=O)O'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
- molecule: Monomer
element: H
position: 19
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
AA0534:
id: AA0534
name: N,N-dimethyl-L-serine
comments: 'For alpha-aino acids, both N-alpha-monomethylation, and N-alpha protonation
and complete trimethylation have been observed, but incomplete dimethylation
has not been reported as the end result of a natural process. Generating Enzyme:
N-terminal RCC1 methyltransferase (EC 2.1.1.-).'
synonyms:
- (2S)-2-(dimethylamino)propanoic acid
- N,N-dimethylserine
identifiers:
- ns: mod
id: MOD:01783
- ns: go
id: GO:0035570
- ns: resid
id: AA0534
structure: OC[C@@H](C(=O)O)N(C)C
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
- molecule: Monomer
element: H
position: 7
AA0384:
id: AA0384
name: N-formyl-L-proline
synonyms:
- 1-formyl-2-pyrrolidinecarboxylic acid
- 1-formylproline
- (2S)-1-formylpyrrolidine-2-carboxylic acid
identifiers:
- ns: mod
id: MOD:00389
- ns: resid
id: AA0384
- ns: go
id: GO:0051364
- ns: cas
id: 13200-83-4
structure: O=CN1CCC[C@H]1C(=O)O
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
- molecule: Monomer
element: H
position: 11
C, P:
id: AA0551
name: L-proline 5-hydroxy-oxazole-4-carbothionic acid
comments: The amino group of the following amino acid forms a thiopeptide bond.
The amino(sulfanyl)methylidene tautomeric form is shown in the diagram and model.
The biosynthesis of this modification from the encoded cysteine peptide has
not been elaborated.
synonyms:
- 5-hydroxy-2-[(2S)-pyrrolidin-2-yl]-1,3-oxazole-4-carbothioic O-acid
- (4Z)-4-[hydroxy(sulfanyl)methylidene]-2-[(2S)-pyrrolidin-2-yl]-1,3-oxazol-5(4H)-one
[tautomer]
identifiers:
- ns: resid
id: AA0551
- ns: mod
id: MOD:01845
- ns: pdb.ligand
id: 66G
structure: '[S-]/C=C/1\N=C(OC1=O)[C@@H]1CCC[NH2+]1'
base_monomers:
- P
- C
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
AA0327:
id: AA0327
name: omega-N-glucosyl-L-arginine
comments: 'Although proposed as the origin for plant starch, the anomeric isomer
was beta, rather than alpha, and only a monosaccharide was observed. Generating
Enzyme: amylogenin glucosyltransferase (EC 2.4.1.-).'
synonyms:
- omega-N-glycosyl-L-arginine
- omega-N-(beta-D-glucosyl)-L-arginine
- (2S)-2-amino-5-(beta-D-glucopyranosyl[imino(methylamino)methyl]amino)pentanoic
acid
- NG-beta-D-glucosylarginine
identifiers:
- ns: go
id: GO:0042543
- ns: mod
id: MOD:00332
- ns: resid
id: AA0327
structure: OC[C@H]1O[C@@H](N/C(=[NH+]\CCC[C@@H](C(=O)O)[NH3+])/N)[C@@H]([C@H]([C@@H]1O)O)O
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
- molecule: Monomer
element: H
position: 19
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
AA0201:
id: AA0201
name: L-isoglutamyl-polyglycine
comments: 'Generating Enzyme: glycine:protein-glutamate gamma-ligase (ADP-forming)
(EC 6.3.2.-); glycine:protein-glutamyl(gamma-polyglycine) N-ligase (ADP-forming)
(EC 6.3.2.-).'
synonyms:
- gamma-glutamylpolyglycineCross-references
- '21343'
- ChEBI
identifiers:
- ns: go
id: GO:0018094
- ns: mod
id: MOD:00206
- ns: chebi
id: CHEBI:21343
- ns: resid
id: AA0201
structure: O=C[C@H](CCC(=O)NCC(=O)[O-])[NH3+]
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
AA0105:
id: AA0105
name: L-cysteine methyl ester
comments: 'The term "carboxyl methylation" applies to this modification. The terms
"carboxy methylation" and "carboxymethylation" are sometimes used incorrectly
for this modification. Since those terms mean "replacement by a methylcarboxylic
acid", they actually refer to a different, artifactual modification. Generating
Enzyme: protein-S-isoprenylcysteine O-methyltransferase (EC 2.1.1.100).'
synonyms:
- mecysteine
- methyl (2R)-2-amino-3-sulfanyl-propanoate
- 2-amino-3-mercaptopropanoic methyl ester
- C
- 2-amino-3-sulfanylpropanoic methyl ester
- methyl L-cysteinate
- methyl (2R)-2-amino-3-sulfanylpropanoate
- o-methylcysteine
identifiers:
- ns: chebi
id: CHEBI:61989
- ns: cas
id: 2485-63-3
- ns: mod
id: MOD:00114
- ns: resid
id: AA0105
- ns: pdb-ccd
id: CMT
- ns: go
id: GO:0018229
- ns: pdb.ligand
id: CMT
structure: COC(=O)[C@H](CS)N
base_monomers:
- C
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
AA0349:
id: AA0349
name: O3-(riboflavin phosphoryl)-L-threonine
synonyms:
- (2S,3R)-2-amino-3-(riboflavin 5'-hydrogen phosphonoxy)butanoic acid
- O3-threonyl FMN
- O3-threonyl flavin mononucleotide
identifiers:
- ns: resid
id: AA0349
- ns: go
id: GO:0050740
- ns: mod
id: MOD:00354
structure: O=c1[nH]c(=O)c2c([nH]1)n(C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O[C@@H]([C@@H](C(=O)O)[NH3+])C)[O-])O)O)O)c1=C[C@H](C(=Cc1n2)C)C
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 28
l_bond_atoms:
- molecule: Monomer
element: N
position: 31
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 30
- molecule: Monomer
element: H
position: 30
l_displaced_atoms:
- molecule: Monomer
element: H
position: 31
- molecule: Monomer
element: H
position: 31
charge: 1
AA0511:
id: AA0511
name: glycyl phospho-5'-adenosine
synonyms:
- (2-aminoacetyl)oxy-([(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy)phosphinic
acid
- ([(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl)-2-aminoethanoate
- glycyl 5'-adenylate
- glycyl adenosine-5'-phosphate
- aminoacetyl [5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl
hydrogen phosphate
- glycyladenylate
- 5'-adenylic-glyinate
- glycine monoanhydride with 5'-adenylic acid
identifiers:
- ns: pdb.ligand
id: AMP
- ns: mod
id: MOD:01614
- ns: resid
id: AA0511
- ns: cas
id: 35985-26-3
structure: NCC(=O)O[P@](=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1NC=N[C@H]2N)[O-]
base_monomers:
- G
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
D, G:
id: AA0410
name: 2-imino-alanine 5-imidazolinone glycine
comments: 'This entry represents the cross-link of the peptide backbone from the
alpha-carboxyl carbon of residue N, an aspartic acid, to the alpha-amino nitrogen
of residue N+2, a glycine, coupled with the formation of a double bond to the
alpha-amino nitrogen of residue N, the loss of a molecule of water, and the
beta-decarboxylation of the aspartic acid. This cross-link is accompanied by
modification of residue N+1. The modified residue N+1 is presented in a separate
entry and is not included in the mass accounting of this entry. The backbone
atoms of residue N+1 are shown in gray in the diagram. Generating Enzyme: autocatalytic.'
synonyms:
- 2-[(4Z)-2-ethanimidoyl-4-[(4-hydroxyphenyl)methylidene]-5-oxo-imidazol-1-yl]ethanoic
acid
- '{(4Z)-2-[(1E)-ethanimidoyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid'
- 2,N-didehydroalanyl-5-imidazolinone glycine
- '[2-(1-iminoethyl)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid'
- 2-(1-iminoethyl)-1-carboxymethyl-1-imidazolin-5-one
- red fluorescent protein zRFP574 chromophore
- (2-ethanimidoyl-5-oxo-4,5-dihydro-1H-imidazol-1-yl)acetic acid
- DYG
- alanyl-5-imidazolinone glycine
- para-hydroxybenzylidene-imidazolidinone chromophore
- 2-imino-alanyl-5-imidazolinone glycine
- '[(4z)-2-[(1z)-ethanimidoyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic
acid'
identifiers:
- ns: pdb.ligand
id: XYG
- ns: mod
id: MOD:00820
- ns: resid
id: AA0410
- ns: pdb-ccd
id: XYG
structure: OC(=O)CN1C(=O)CN=C1C(=N)C
base_monomers:
- D
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
AA0517:
id: AA0517
name: N-(12-oxomyristoyl)-L-cysteine
synonyms:
- 2-(12-oxotetradecanoyl)amino-3-sulfanylpropanoic acid
- N-(12-oxotetradecanoyl)cysteine
identifiers:
- ns: resid
id: AA0517
- ns: mod
id: MOD:01691
structure: CCC(=O)CCCCCCCCCCC(=O)N[C@H](C(=O)O)CS
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
AA0157:
id: AA0157
name: O4'-glycosyl-L-tyrosine
comments: 'The carbohydrate is glucose, the origin for glycogen. One to eleven
alpha-1,4-linked glucose units may be auto-catalytically attached. See also
RESID:AA0577 for other O-glycosylated tyrosines. Generating Enzyme: glycogenin
glucosyltransferase (EC 2.4.1.186).'
synonyms:
- (2S)-2-amino-3-(4-alpha-D-glucopyranosyloxy)phenylpropanoic acid
- O4'-glycosyl-L-tyrosine
identifiers:
- ns: go
id: GO:0006493
- ns: mod
id: MOD:00166
- ns: resid
id: AA0157
structure: OC[C@H]1O[C@H](Oc2ccc(cc2)C[C@@H](C(=O)O)[NH3+])[C@@H]([C@H]([C@@H]1O)O)O
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
- molecule: Monomer
element: H
position: 20
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
AA0302:
id: AA0302
name: L-aspartimide
comments: This modification is autocatalytically produced from the carboxyl-terminal
asparagine of spliced inteins. This modification is produced by the MccB enzyme
as an intermediate in the process of biosynthesizing (3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine.
See RESID:AA0328.
synonyms:
- ASI
- 2-amino-butanimide
- (3S)-3-amino-2,5-pyrrolidinedione
- L-3-aminosuccinimide [misnomer]
- N
- L-2-aminosuccinimide
- l-3-aminosuccinimide
- (3S)-3-aminopyrrolidine-2,5-dione
- L-asparaginimide
- alpha-aminosuccinimide
identifiers:
- ns: cas
id: 5615-80-5
- ns: pdb-ccd
id: SNN
- ns: mod
id: MOD:00307
- ns: resid
id: AA0302
- ns: pdb.ligand
id: SNN
- ns: go
id: GO:0019801
structure: O=C1C[C@@H](C(=O)N1)N
base_monomers:
- N
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
AA0580:
id: AA0580
name: 3-hydroxy-L-histidine
comments: 'This modified histidine has been found in an ankyrin repeat domain
in a position occupied by asparagine in homologous sequences. The diastereomeric
form has not been determined. Generating Enzyme: peptide-histidine beta-dioxygenase
(EC 1.14.11.-).'
synonyms:
- (2S)-2-amino-3-hydroxy-3-(1H-imidazol-4-yl)propanoic acid
identifiers:
- ns: resid
id: AA0580
- ns: mod
id: MOD:01920
structure: N[C@H](C(=O)O)[C@H](c1c[nH]cn1)O
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0481:
id: AA0481
name: L-asparagine thiazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-cysteine
cyclase (EC 4.2.1.-); peptidyl-thiazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-[1,3-bisazanyl-3-oxopropyl]-1,3-thiazole-4-carboxylic acid
- 2-[(1S)-1,3-diamino-3-oxopropyl]-1,3-thiazole-4-carboxylic acid
identifiers:
- ns: resid
id: AA0481
- ns: mod
id: MOD:01404
structure: NC(=O)C[C@@H](c1scc(n1)C(=O)O)N
base_monomers:
- N
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
AA0060:
id: AA0060
name: N-palmitoyl-L-cysteine
comments: 'In bacteria, the enzyme producing this modification may use a mixture
of saturated and unsaturated fatty acids and act in close association with the
enzyme producing S-diacylglycerol-L-cysteine (see RESID:AA0107). The signal
peptide that is cleaved immediately before the modified cysteine typically ends
in the motif [ILMV]X[AGS]C. In eukaryotes, the enzyme acts in the absence of
modification of the cysteine thiol and may proceed after initial S-acylation
(see RESID:AA0106) through a cyclic intermediate to the final N-acyl form. The
eukaryotic enzyme appears to act more efficiently following formation of a carboxyl-terminal
cholesterol ester (see RESID:AA0309). This modification should not be confused
with S-palmitoyl-cysteine (see RESID:AA0106). Generating Enzyme: protein-cysteine
N-palmitoyltransferase (EC 2.3.1.-).'
synonyms:
- N-(1-oxahexadecyl)-L-cysteine
- 2-hexadecanoylamino-3-mercaptopropanoic acid
- 2-hexadecanamido-3-sulfanylpropanoic acid
- (2R)-2-hexadecanoylamino-3-sulfanylpropanoic acid
identifiers:
- ns: cas
id: 67603-49-0
- ns: mod
id: MOD:00069
- ns: resid
id: AA0060
- ns: go
id: GO:0018009
structure: CCCCCCCCCCCCCCCC(=O)N[C@H](C(=O)O)CS
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 21
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
r_displaced_atoms:
- molecule: Monomer
element: O
position: 23
- molecule: Monomer
element: H
position: 23
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
AA0212:
id: AA0212
name: O4-arabinosyl-L-hydroxyproline
comments: 'See also RESID:AA0389 and RESID:AA0390 for other O4-glycosylated 4-hydroxyprolines.
Generating Enzyme: [protein]-hydroxyproline O-arabinosyltransferase (EC 2.4.1.-).'
synonyms:
- beta-arabinofuranosyl-4-hydroxyproline
- (2S,4R)-4-(beta-L-arabinofuranosyloxy)pyrrolidine-2-carboxylic acid
- 4-(beta-L-arabinofuranosyloxy)proline
- O4-glycosyl-hydroxyproline
identifiers:
- ns: go
id: GO:0006493
- ns: mod
id: MOD:00217
- ns: resid
id: AA0212
structure: OC[C@@H]1O[C@H]([C@@H]([C@H]1O)O)O[C@H]1C[NH2+][C@@H](C1)C(=O)O
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 24
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 26
- molecule: Monomer
element: H
position: 26
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0482:
id: AA0482
name: L-proline thiazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-cysteine
cyclase (EC 4.2.1.-); peptidyl-thiazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-[(2S)-pyrrolidin-2-yl]-1,3-thiazole-4-carboxylic acid
identifiers:
- ns: resid
id: AA0482
- ns: mod
id: MOD:01405
structure: OC(=O)c1csc(n1)[C@@H]1CCC[NH2+]1
base_monomers:
- P
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
AA0306:
id: AA0306
name: L-cysteine coenzyme A disulfide
synonyms:
- coenzyme A L-cysteine mixed disulfide
- (2R)-2-amino-3-(2-((3-(((2R)-2,4-dihydroxy-3,3-dimethyl-1-oxobutyl)amino)-1-oxopropyl)amino)ethyl)dithio-propanoic
acid 4'-ester with adenosine 5'-(trihydrogen diphosphate) 3'-(dihydrogen phosphate)
identifiers:
- ns: go
id: GO:0019703
- ns: resid
id: AA0306
- ns: mod
id: MOD:00311
structure: O=C(NCCSSC[C@@H](C(=O)O)[NH3+])CCNC(=O)[C@@H](C(COP(=O)(OP(=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1OP(=O)([O-])[O-])O)n1cnc2c1ncnc2N)[O-])[O-])(C)C)O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
AA0309:
id: AA0309
name: glycine cholesterol ester
comments: This modification occurs at the carboxyl end released during autolytic
cleavage.
synonyms:
- hedgehog lipophilic adduct
- cholesteryl glycinate
- glycine cholest-5-en-3beta-ol ester
identifiers:
- ns: go
id: GO:0019708
- ns: mod
id: MOD:00314
- ns: resid
id: AA0309
- ns: cas
id: 57-88-5
structure: NCC(=O)O[C@H]1CC[C@]2(C(=CC[C@@H]3[C@@H]2CC[C@]2([C@H]3CC[C@@H]2[C@@H](CCCC(C)C)C)C)C1)C
base_monomers:
- G
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0079:
id: AA0079
name: O-palmitoyl-L-threonine
comments: The palmitate represents a mixture of saturated and unsaturated fatty
acids.
synonyms:
- O3-palmitoyl-threonine
- (2S,3R)-2-amino-3-(hexadecanoyloxy)butanoic acid
- L-threonine hexadecanoate ester
- threonine palmitate ester
identifiers:
- ns: mod
id: MOD:00088
- ns: cas
id: 88467-30-5
- ns: resid
id: AA0079
- ns: go
id: GO:0018220
structure: CCCCCCCCCCCCCCCC(=O)O[C@@H]([C@@H](C(=O)O)[NH3+])C
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 23
l_bond_atoms:
- molecule: Monomer
element: N
position: 26
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 25
- molecule: Monomer
element: H
position: 25
l_displaced_atoms:
- molecule: Monomer
element: H
position: 26
- molecule: Monomer
element: H
position: 26
charge: 1
AA0155:
id: AA0155
name: O-(N-acetylaminogalactosyl)-L-threonine
comments: 'See also RESID:AA0247, RESID:AA0399, RESID:AA0401, RESID:AA0403, RESID:AA0405,
and RESID:AA0515 for other O-glycosylated threonines. Generating Enzyme: polypeptide
N-acetylgalactosaminyltransferase (EC 2.4.1.41).'
synonyms:
- O3-(N-acetylgalactosaminyl)threonine
- (2S,3R)-2-amino-3-(2-acetamido-2-deoxy-alpha-D-galactopyranosyloxy)butanoic
acid
- mucin type O-glycosylthreonine
identifiers:
- ns: resid
id: AA0155
- ns: chebi
id: CHEBI:53605
- ns: pdb.ligand
id: GTH
- ns: mod
id: MOD:00164
- ns: go
id: GO:0006493
structure: OC[C@H]1O[C@@H](O[C@@H]([C@@H](C(=O)O)[NH3+])C)[C@@H]([C@H]([C@H]1O)O)NC(=O)C
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0554:
id: AA0554
name: L-threonine 5-hydroxy-oxazole-4-carbonthionic acid
comments: The amino group of the following amino acid forms a thiopeptide bond.
This is an amino(sulfanyl)methylidene in the tautomeric form, which is shown
in the diagram and model.
synonyms:
- 2-[(1S,2R)-1-amino-2-hydroxypropyl]-5-hydroxy-1,3-oxazole-4-carbothioic O-acid
- (4Z)-2-[(1S,2R)-1-amino-2-hydroxypropyl]-4-(sulfanylmethylidene)-1,3-oxazol-5(4H)-one
[tautomer]
identifiers:
- ns: mod
id: MOD:01878
- ns: resid
id: AA0554
structure: '[S-]/C=C/1\N=C(OC1=O)[C@H]([C@H](O)C)[NH3+]'
base_monomers:
- T
- C
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
AA0239:
id: AA0239
name: L-cysteine oxazoline-4-carboxylic acid
comments: 'Formed by the condensation of a serine hydroxyl with the carbonyl of
the preceding residue. Generating Enzyme: peptidyl-serine cyclase (EC 4.2.1.-).'
synonyms:
- (4S)-2-[(1R)-1-amino-2-sulfanylethyl]-4,5-dihydro-1,3-oxazole-4-carboxylic acid
- 2-[1-azanyl-2-sulfanylethyl]-4,5-dihydro-1,3-oxazole-4-carboxylic acid
identifiers:
- ns: mod
id: MOD:00244
- ns: go
id: GO:0018133
- ns: resid
id: AA0239
structure: OC(=O)[C@@H]1COC(=N1)[C@@H]([NH3+])CS
base_monomers:
- S
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
AA0347:
id: AA0347
name: L-glutamyl 5-omega-hydroxyceramide ester
comments: This lipid modification is thought to span the lipid bilayer. A representative
structure is shown.
synonyms:
- (S)-2-amino-5-[30-((2S,3R,4E)-1,3-dihydroxyicos-4-en-2-ylamino)-30-oxotriacontan-1-yloxy]-5-oxopentanoic
acid
- 2-[30-(isoglutamyloxy)triacontanoyl]icosasphingosine
identifiers:
- ns: mod
id: MOD:00352
- ns: resid
id: AA0347
- ns: go
id: GO:0050496
structure: CCCCCCCCCCCCCCC/C=C/[C@H]([C@@H](NC(=O)CCCCCCCCCCCCCCCCCCCCCCCCCCCCCOC(=O)CC[C@@H](C(=O)O)[NH3+])CO)O
base_monomers:
- Q
r_bond_atoms:
- molecule: Monomer
element: C
position: 61
l_bond_atoms:
- molecule: Monomer
element: N
position: 64
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 63
- molecule: Monomer
element: H
position: 63
l_displaced_atoms:
- molecule: Monomer
element: H
position: 64
- molecule: Monomer
element: H
position: 64
charge: 1
AA0228:
id: AA0228
name: N6-(phospho-5'-guanosine)-L-lysine
synonyms:
- N(zeta)-5'-guanylic-lysine
- lysine guanosine-5'-monophosphate
- (2S)-2-amino-6-{[(S)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]amino}hexanoic
acid (non-preferred name)
- (2S)-2-amino-6-[[[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]amino]hexanoic
acid
- epsilon-5'-guanylic-L-lysine
- 5'-guanylic-N6-L-lysine
- K
- N6-(5'-guanylyl)-lysine
- L-lysine monoanhydride with 5'-guanylic acid
- (2S)-2-amino-6-(5'-guanosine phosphonamino)hexanoic acid
- N6-L-lysine 5'-guanosine phosphoramidester
identifiers:
- ns: go
id: GO:0018261
- ns: pdb-ccd
id: GPL
- ns: pdb.ligand
id: GPL
- ns: resid
id: AA0228
- ns: mod
id: MOD:00233
structure: OC(=O)[C@H](CCCCN[P@](=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1nc(N)[nH]c2=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 39
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 39
- molecule: Monomer
element: H
position: 39
charge: 1
AA0408:
id: AA0408
name: 3'-geranyl-2',3'-dihydro-2',N2-cyclo-L-tryptophan
synonyms:
- (2S,3R)-3-geranyl-2,3-dihydro-2,N(alpha)-cyclo-L-tryptophan
- (2S,3aR,8aS)-3a-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-1,2,3,3a,8,8a-hexahydropyrrolo[2,3-b]indole-2-carboxylic
acid
identifiers:
- ns: mod
id: MOD:00817
- ns: resid
id: AA0408
- ns: chebi
id: CHEBI:35304
structure: C/C(=C\C[C@]12C[C@H](N[C@H]1Nc1c2cccc1)C(=O)O)/CCC=C(C)C
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 19
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 21
- molecule: Monomer
element: H
position: 21
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
AA0613:
id: AA0613
name: 5-glutamyl N2-ornithine
comments: This modification is probably produced on the C-terminal glutamic acid
of a carrier protein as one of a series of intermediates.
synonyms:
- 4-amino-5-[(4-amino-1-carboxy-butyl)amino]-5-ketovaleric acid
- gamma-glutamylornithine
- N2-(L-isoglutamyl)-L-ornithine
- (2S)-5-amino-2-[(4S)-4-amino-4-carboxybutanamido]pentanoic acid
- 4-amino-5-[(4-amino-1-carboxy-butyl)amino]-5-oxopentanoic acid
- (2S)-5-amino-2-([(4S)-4-amino-4-carboxybutanoyl]amino)pentanoic acid
- N2-(gamma-glutamyl)ornithine
identifiers:
- ns: cas
id: 56523-61-6
- ns: mod
id: MOD:01971
- ns: resid
id: AA0613
structure: O=C[C@H](CCC(=O)N[C@H](C(=O)[O-])CCC[NH3+])[NH3+]
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
S, T:
id: AA0575
name: L-serine 5-methyloxazoline-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-threonine
cyclase (EC 4.2.1.-).'
synonyms:
- 2-[(1S)-1-amino-2-hydroxyethyl]-5-methyl-1,3-oxazoline-4-carboxylic acid
- 2-[(1S)-1-azanyl-2-hydroxyethyl]-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxylic
acid
- 2-[(1S)-1-amino-2-hydroxyethyl]-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxylic
acid
identifiers:
- ns: mod
id: MOD:01904
- ns: resid
id: AA0575
structure: OC[C@@H](C1=N[C@@H]([C@H](O1)C)C(=O)O)[NH3+]
base_monomers:
- S
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
AA0050:
id: AA0050
name: N-acetyl-L-proline
synonyms:
- (2S)-1-acetyl-2-pyrrolidinecarboxylic acid
- 1-acetylproline
- acetylproline
- N-acetylproline
identifiers:
- ns: cas
id: 68-95-1
- ns: chebi
id: CHEBI:21560
- ns: go
id: GO:0017197
- ns: mod
id: MOD:00059
- ns: resid
id: AA0050
structure: CC(=O)N1CCC[C@H]1C(=O)O
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
AA0464:
id: AA0464
name: O3-methyl-L-threonine
synonyms:
- (2S,3R)-2-amino-3-methoxybutanoic acid
- O-methyl-L-threonine
- T
- o-methyl-l-threonine
- threonine methyl ether
- O-methyl threonine
- (2S,3R)-2-amino-3-methoxy-butanoic acid
identifiers:
- ns: resid
id: AA0464
- ns: pdb-ccd
id: OLT
- ns: pdb.ligand
id: OLT
- ns: mod
id: MOD:01387
- ns: cas
id: 4385-90-4
structure: CO[C@@H]([C@@H](C(=O)O)[NH3+])C
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
AA0227:
id: AA0227
name: N6-(phospho-5'-adenosine)-L-lysine
synonyms:
- 5'-adenylic-N6-L-lysine
- (2S)-2-amino-6-(5'-adenosine phosphonamino)hexanoic acid
- L-lysine monoanhydride with 5'-adenylic acid
- N(zeta)-5'-adenylic-L-lysine
- epsilon-5'-adenylic-L-lysine
- N6-L-lysine 5'-adenosine phosphoramidester
identifiers:
- ns: pdb.ligand
id: AMP
- ns: cas
id: 35985-27-4
- ns: resid
id: AA0227
- ns: go
id: GO:0018116
- ns: mod
id: MOD:00232
structure: OC(=O)[C@H](CCCCNP(=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 37
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 37
- molecule: Monomer
element: H
position: 37
charge: 1
AA0114:
id: AA0114
name: N6-carboxy-L-lysine
comments: 'N6-carboxylysine can be produced by artifactual, catalytic or auto-catalytic
processes. Generating Enzyme: ribulose-bisphosphate carboxylase activase (EC
6.3.4.-); urease activase (EC 6.3.4.-).'
synonyms:
- lysine nz-carboxylic acid
- lysine NZ-carboxylic acid
- (2S)-2-amino-6-(carboxyamino)hexanoic acid
- 2-amino-6-carbamic hexanoic acid
- K
- N6-carboxylysine
- N~6~-carboxy-L-lysine
- N6-carbamyllysine [misnomer]
- (2S)-2-azanyl-6-(carboxyamino)hexanoic acid
identifiers:
- ns: pdb.ligand
id: FMT
- ns: resid
id: AA0114
- ns: go
id: GO:0018235
- ns: pdb-ccd
id: KCX
- ns: mod
id: MOD:00123
- ns: cas
id: 45101-60-8
- ns: chebi
id: CHEBI:49185
structure: '[O-]C(=O)NCCCC[C@@H](C(=O)O)[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
AA0031:
id: AA0031
name: 2-pyrrolidone-5-carboxylic acid
comments: 'This modification can form artifactually from amino-terminal glutamine
under mildly acid conditions, and from amino-terminal glutamic acid under very
acid or anhydrous conditions. The presumed enzyme in Aplysia neurons has not
been characterized. The reaction probably requires concomitant hydrolysis of
a compound such as ATP. Generating Enzyme: glutaminyl-peptide cyclotransferase
(EC 2.3.2.5) #link GLN.'
synonyms:
- (2S)-5-oxopyrrolidine-2-carboxylic acid
- PCA
- (2S)-5-oxo-2-pyrrolidinecarboxylic acid
- 5-oxoproline
- 2-oxopyrrolidine-5-carboxylic acid
- 5-pyrrolidone-2-carboxylic acid
- E
- pyroglutamic acid
- 5-oxopyrrolidine-2-carboxylic acid
- 5-oxo-L-proline
identifiers:
- ns: pdb-ccd
id: PCA
- ns: cas
id: 98-79-3
- ns: chebi
id: CHEBI:30652
- ns: resid
id: AA0031
- ns: mod
id: MOD:00420
- ns: go
id: GO:0017186
- ns: mod
id: MOD:00040
- ns: pdb.ligand
id: PCA
structure: O=C1CC[C@H](N1)C(=O)O
base_monomers:
- E
- Q
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
AA0615:
id: AA0615
name: N6-(3-phosphoglyceryl)-L-lysine
comments: 'Generating Enzyme: autocatalytic.'
synonyms:
- (2S)-2-amino-6-[(2R)-2-hydroxy-3-(phosphonooxy)propanamido]hexanoic acid
- 3-phosphoglyceryl-lysine
- (2S)-2-amino-6-([(2R)-2-hydroxy-3-(phosphonooxy)propanoyl]amino)hexanoic acid
identifiers:
- ns: resid
id: AA0615
- ns: mod
id: MOD:01973
structure: O=C([C@@H](COP(=O)([O-])[O-])O)NCCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 19
l_bond_atoms:
- molecule: Monomer
element: N
position: 22
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 21
- molecule: Monomer
element: H
position: 21
l_displaced_atoms:
- molecule: Monomer
element: H
position: 22
- molecule: Monomer
element: H
position: 22
charge: 1
AA0335:
id: AA0335
name: S-amidino-L-cysteine
comments: 'Generating Enzyme: glycine amidinotransferase (EC 2.1.4.1).'
synonyms:
- (2R)-2-amino-3-(carbamimidoylsulfanyl)propanoic acid
- S-amidinocysteine
- 2-amino-3-amidinothiopropanoic acid
- alpha-amino-beta-amidinothiopropionic acid
- beta-(S-isothiourea)alanine
- 2-amino-3-amidinosulfanylpropanoic acid
- beta-amidinothioalanine
identifiers:
- ns: go
id: GO:0046894
- ns: mod
id: MOD:00340
- ns: resid
id: AA0335
structure: NC(=[NH2])SC[C@@H](C(=O)O)N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
AA0236:
id: AA0236
name: N4-hydroxymethyl-L-asparagine
comments: N4-methyl-L-asparagine (see RESID:AA0070) was found at a homologous
position in the closely related species Anabaena variabilis. Since the peptide
containing this modification was obtained by enzymatic cleavage, not cyanogen
bromide cleavage, it could have experienced oxidation of the following methionine
residue, leading to the erroneous attribution of a mass of 29 for the modification
rather than 14.
synonyms:
- N(gamma)-hydroxymethylasparagine
- (2S)-2-amino-4-[(hydroxymethyl)amino]-4-oxobutanoic acid
- beta-hydroxymethylasparagine
- 2-amino-N4-hydroxymethylbutanediamic acid
- N4-hydroxymethylasparagine
identifiers:
- ns: go
id: GO:0018311
- ns: resid
id: AA0236
- ns: mod
id: MOD:00241
structure: OCNC(=O)C[C@@H](C(=O)O)N
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
- molecule: Monomer
element: H
position: 11
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
AA0078:
id: AA0078
name: N6-myristoyl-L-lysine
comments: 'Generating Enzyme: peptidyl-lysine N6-myristoyltransferase (EC 2.3.1.-).'
synonyms:
- 2-amino-6-(tetradecanamido)hexanoic acid
- N(zeta)-myristoyllysine
- (2S)-2-azanyl-6-(tetradecanoylamino)hexanoic acid
- n~6~-tetradecanoyl-l-lysine
- epsilon-myristoyllysine
- N~6~-tetradecanoyl-L-lysine
- N6-(1-oxotetradecyl)-L-lysine
- (2S)-2-amino-6-(tetradecanoylamino)hexanoic acid
identifiers:
- ns: resid
id: AA0078
- ns: go
id: GO:0018028
- ns: chebi
id: CHEBI:21894
- ns: cas
id: 62471-07-2
- ns: mod
id: MOD:00087
- ns: pdb-ccd
id: MYK
- ns: pdb.ligand
id: MYK
structure: CCCCCCCCCCCCCC(=O)NCCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 23
l_bond_atoms:
- molecule: Monomer
element: N
position: 26
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 25
- molecule: Monomer
element: H
position: 25
l_displaced_atoms:
- molecule: Monomer
element: H
position: 26
- molecule: Monomer
element: H
position: 26
charge: 1
AA0371:
id: AA0371
name: 1'-(phospho-5'-adenosine)-L-histidine
comments: The phosphoramide bond is probably formed with the tele-nitrogen of
histidine in most cases.
synonyms:
- N(tau)-5'-adenylic-L-histidine
- N1'-adenylylated histidine
- (2S)-2-amino-3-[1-(5'-adenosine phosphono)imidazol-4-yl]propanoic acid
- L-histidine 5'-adenosine phosphoramidester
- tele-5'-adenylic-L-histidine
- L-histidine monoanhydride with 5'-adenylic acid
identifiers:
- ns: pdb.ligand
id: AMP
- ns: go
id: GO:0051111
- ns: mod
id: MOD:00376
- ns: resid
id: AA0371
structure: OC(=O)[C@@H](Cc1ncn(c1)[P@@](=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1NC=N[C@H]2N)[O-])[NH3+]
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 39
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 39
- molecule: Monomer
element: H
position: 39
charge: 1
AA0312:
id: AA0312
name: N6-3,4-didehydroretinylidene-L-lysine
comments: The all-trans form is shown. Light-induced interconversion with the
11-cis (4Z) form in porphyropsin and cyanopsin is utilized for light sensing
in some animals. This modification has been detected but not located by sequencing
in proteins. It may be substituted for retinal (see RESID:AA0120) in opsin.
synonyms:
- N6-3-dehydroretinal-L-lysine
- N6-3-dehydroretinyl-lysine
- (S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexa-1,3-dien-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic
acid
identifiers:
- ns: resid
id: AA0312
- ns: go
id: GO:0019931
- ns: mod
id: MOD:00317
- ns: cas
id: 472-87-7
structure: C[C@@H](/C=C/C=C(/C=C/C1=C(C)C=CCC1(C)C)\C)/C=C/[NH2+]CCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 31
l_bond_atoms:
- molecule: Monomer
element: N
position: 34
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 33
- molecule: Monomer
element: H
position: 33
l_displaced_atoms:
- molecule: Monomer
element: H
position: 34
- molecule: Monomer
element: H
position: 34
charge: 1
AA0030:
id: AA0030
name: 4-hydroxy-L-proline
comments: 'Generating Enzyme: procollagen-proline dioxygenase (EC 1.14.11.2);
hypoxia-inducible factor-proline dioxygenase (EC 1.14.11.29).'
synonyms:
- (4R)-4-hydroxy-L-proline
- gamma-hydroxypyrrolidine-alpha-carboxylic acid
- 4-hydroxyproline
- P
- L-threo-4-hydroxyproline
- 4-trans-hydroxy-L-proline
- (2S,4R)-4-hydroxypyrrolidine-2-carboxylic acid
identifiers:
- ns: pdb.ligand
id: HYP
- ns: chebi
id: CHEBI:61965
- ns: resid
id: AA0030
- ns: pdb-ccd
id: HYP
- ns: go
id: GO:0018401
- ns: mod
id: MOD:00039
- ns: cas
id: 51-35-4
structure: O[C@H]1C[NH2+][C@@H](C1)C(=O)O
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
E, G:
id: AA0378
name: 2-imino-glutamic acid 5-imidazolinone glycine
comments: 'This entry represents the cross-link of the peptide backbone from the
alpha-carboxyl carbon of residue N, a glutamic acid, to the alpha-amino nitrogen
of residue N+2, a glycine, coupled with the formation of a double bond to the
alpha-amino nitrogen of residue N, and the loss of a molecule of water. This
cross-link is accompanied by modification of residue N+1. The modified residue
N+1 is presented in a separate entry and is not included in the mass accounting
of this entry. The backbone atoms of residue N+1 are shown in gray in the diagram.
Generating Enzyme: autocatalytic.'
synonyms:
- 4-[(4z)-1-(carboxymethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-2-yl]-4-iminobutanoic
acid
- 2-imino-glutamyl-5-imidazolinone glycine
- (4Z)-4-[(4E)-1-(carboxymethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-2-yl]-4-iminobutanoic
acid
- 4-azanylidene-4-[(4E)-1-(carboxymethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-2-yl]butanoic
acid
- EYG
- 2,N-didehydroglutamyl-5-imidazolinone glycine
- 4-[1-(carboxymethyl)-5-oxo-4,5-dihydro-1H-imidazol-2-yl]-4-iminobutanoic acid
- para-hydroxybenzylidene-imidazolidinone chromophore
- '[2-(3-carboxy-1-iminopropyl)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid'
- 2-(3-carboxy-1-iminopropyl)-1-carboxymethyl-1-imidazolin-5-one
identifiers:
- ns: pdb-ccd
id: CRU
- ns: resid
id: AA0378
- ns: go
id: GO:0051358
- ns: pdb.ligand
id: CRU
- ns: mod
id: MOD:00383
structure: O=CCN1C(=O)CN=C1C(=N)CCC(=O)[O-]
base_monomers:
- E
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
C, V:
id: AA0468
name: L-valine 5-(methoxymethyl)thiazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-cysteine
cyclase (EC 4.2.1.-); peptidyl-thiazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-[(1S)-1-amino-2-methylpropyl]-5-(methoxymethyl)-1,3-thiazole-4-carboxylic
acid
- 2-[1-azanyl-2-methylpropyl]-5-(methoxymethyl)-1,3-thiazole-4-carboxylic acid
identifiers:
- ns: resid
id: AA0468
- ns: mod
id: MOD:01391
structure: COCc1sc(nc1C(=O)O)[C@H](C(C)C)[NH3+]
base_monomers:
- V
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
- molecule: Monomer
element: H
position: 11
AA0406:
id: AA0406
name: O-xylosyl-L-serine
comments: One glycosylated serine with weak electron density was modeled as O3-alpha-xylosylserine,
while O3-alpha-mannosyl serine and threonine were modeled at ten other positions.
The authors do not discuss this exception or provide chemical evidence for it.
Since an O3-xylosyl serine modification has not been reported in any other fungal
proteins, the modification is probably also an O3-alpha-mannosyl serine (see
RESID:AA0402). See also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210,
RESID:AA0291, RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400,
RESID:AA0402, RESID:AA0404, and RESID:AA0422 for other O-glycosylated serines.
synonyms:
- O3-xylosylserine
- O-(beta-D-xylopyranosyl)-L-serine
- (2S)-2-amino-3-(alpha-D-xylopyranosyloxy)propanoic acid
- O-glycosylserine
identifiers:
- ns: resid
id: AA0406
- ns: mod
id: MOD:00814
- ns: pdb.ligand
id: XYS
- ns: cas
id: 6050-71-1
structure: OC(=O)[C@H](CO[C@H]1OC[C@H]([C@@H]([C@H]1O)O)O)[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
AA0234:
id: AA0234
name: S-methyl-L-cysteine
comments: 'For methylated--DNA--[protein]-cysteine S-methyltransferase (EC 2.2.1.63),
the Enzyme Commission acknowledges that "This enzyme catalyses only one turnover
and therefore is not strictly catalytic." Generating Enzyme: autocatalytic;
methylated--DNA--[protein]-cysteine S-methyltransferase (EC 2.2.1.63); protein-cysteine
methyltransferase, NleE (EC 2.2.1.-).'
synonyms:
- (2R)-2-amino-3-methylsulfanyl-propanoic acid
- s-methylcysteine
- (R)-2-amino-3-(methylsulfanyl)propanoic acid
- C
- S-methyl-L-cysteine
- L-3-(methylthio)alanine
identifiers:
- ns: resid
id: AA0234
- ns: pdb.ligand
id: SMC
- ns: go
id: GO:0018125
- ns: mod
id: MOD:00239
- ns: pdb-ccd
id: SMC
- ns: cas
id: 1187-84-4
structure: CSC[C@H]([NH3+])C(=O)O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
AA0396:
id: AA0396
name: 3-(S-L-cysteinyl)-L-tyrosine
comments: This modification should not be confused with 3'-(S-L-cysteinyl)-L-tyrosine
(see RESID:AA0113).
synonyms:
- (2S,3R)-2-amino-3-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-3-(4-hydroxyphenyl)propanoic
acid
- 2-amino-3-(2-amino-2-carboxyethylthio)-3-(4-hydroxyphenyl)propanoic acid
- S-(tyros-3'-yl)cysteine
identifiers:
- ns: resid
id: AA0396
- ns: mod
id: MOD:00803
structure: O=C[C@H]([C@@H](c1ccc(cc1)O)SC[C@@H](C(=O)O)[NH3+])[NH3+]
base_monomers:
- Y
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
- molecule: Monomer
element: H
position: 20
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
AA0558:
id: AA0558
name: S-(spermidinoglutathion-S-yl)-L-cysteine
synonyms:
- L-gamma-glutamyl-[S-(L-cystein-S-yl)]-L-cysteinyl-N-{3-[(4-aminobutyl)amino]propyl}glycinamide
- cysteine glutathionylspermidine disulfide
- (2R)-2-amino-3-([(2R)-2-([(4S)-4-amino-4-carboxybutanoyl]amino)-2-([2-([3-([4-aminobutyl]amino)propyl]carbamoyl)methyl]carbamoyl)ethyl]disulfanyl)propanoic
acid
identifiers:
- ns: chebi
id: CHEBI:16613
- ns: pdb.ligand
id: TS5
- ns: resid
id: AA0558
- ns: cas
id: 33932-35-3
- ns: mod
id: MOD:01848
structure: '[NH3+]CCCC[NH2+]CCCNC(=O)CNC(=O)[C@@H](NC(=O)CC[C@@H](C(=O)[O-])[NH3+])CSSC[C@@H](C=O)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 31
l_bond_atoms:
- molecule: Monomer
element: N
position: 34
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 33
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 34
- molecule: Monomer
element: H
position: 34
charge: 1
AA0256:
id: AA0256
name: O4'-(phospho-5'-uridine)-L-tyrosine
comments: 'Generating Enzyme: uridylyltransferase (EC 2.7.7.59).'
synonyms:
- hydrogen 5'-uridylate tyrosine ester
- O4'-L-tyrosine 5'-uridine phosphodiester
- (S)-2-amino-3-[4-(5'-uridine phosphonoxy)phenyl]propanoic acid
- 5'-uridylic-O-tyrosine
identifiers:
- ns: go
id: GO:0018165
- ns: mod
id: MOD:00261
- ns: resid
id: AA0256
structure: OC(=O)[C@H](Cc1ccc(cc1)O[P@@](=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1ccc(=O)[nH]c1=O)[O-])[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 39
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 39
- molecule: Monomer
element: H
position: 39
charge: 1
AA0622:
id: AA0622
name: 2-(L-cystein-S-yl)-asparagine
synonyms:
- alpha-(L-cystein-S-yl)-D-asparagine
- (2S)-2,4-diamino-2-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-4-oxobutanoic acid
identifiers:
- ns: pdb.ligand
id: DSG
- ns: mod
id: MOD:01985
- ns: resid
id: AA0622
structure: O=C[C@H](CS[C@](C(=O)O)(CC(=O)N)N)[NH3+]
base_monomers:
- N
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
K, K:
id: AA0430
name: L-dehydrolysinonorleucine
comments: 'Although it should not be possible to distinguish dehydrolysinonorleucine
from lysinonorleucine in the X-ray structure, the cross-link was probably not
reduced. After the oxidation of a lysine to allysine (see RESID:AA0121), this
cross-link forms spontaneously with a Schiff-base reaction. In this aleatoric
modification two peptide chains may be crosslinked with the peptides contributing
a lysine in either biosynthetic position. The lysines forming the cross-link
may also be hydroxylated and glycosylated (see RESID:AA0028 and RESID:AA0153).
Generating Enzyme: lysyl oxidase (EC 1.4.3.13).'
synonyms:
- dehydrolysylnorleucine
- dehydrolysinorleucine [misspelling]
- 6-(N6-L-didehydrolysino)-L-norleucine
- didehydrolysinonorleucine
- N6-[(5S)-5-amino-5-carboxypentylidene]-L-lysine
- (2S)-2-amino-6-([(5S)-5-amino-5-carboxypentylidene]amino)hexanoic acid
identifiers:
- ns: resid
id: AA0430
- ns: chebi
id: CHEBI:64748
- ns: cas
id: 31504-14-0
- ns: mod
id: MOD:01176
structure: O=C[C@H](CCCC[NH2+]CCCC[C@@H](C(=O)O)[NH3+])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
- molecule: Monomer
element: H
position: 20
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
AA0273:
id: AA0273
name: 2-methyl-L-glutamine
synonyms:
- (2S)-2,5-diamino-2-methyl-5-oxo-pentanoic acid
- 2-methylglutamine
- 2-methyl-L-glutamine
- 2-methyl-glutamine
- alpha-methylglutamine
- Q
- (S)-2-amino-2-methylpentanediamic acid
identifiers:
- ns: go
id: GO:0018361
- ns: cas
id: 4247-16-9
- ns: pdb.ligand
id: MGN
- ns: resid
id: AA0273
- ns: pdb-ccd
id: MGN
- ns: mod
id: MOD:00278
structure: NC(=O)CC[C@@](C(=O)O)([NH3+])C
base_monomers:
- Q
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
AA0272:
id: AA0272
name: 5-methyl-L-arginine
comments: This modification should not be confused with N5-methylarginine (see
RESID:AA0305). In methyl-coenzyme M reductase the arginine 5-methyl group is
derived from S-adenosyl-methionine and is not produced as a side reaction of
the enzyme.
synonyms:
- 2-amino-5-guanidinohexanoic acid
- amino{[(1S,4S)-4-amino-4-carboxy-1-methylbutyl]amino}methaniminium
- 5-methyl-arginine
- (2S,5S)-2-amino-5-carbamimidamidohexanoic acid
- delta-methylarginine
- R
- 4-methylarginine [misnomer]
- '[amino-[[(2S,5S)-5-amino-6-hydroxy-6-oxo-hexan-2-yl]amino]methylidene]azanium'
identifiers:
- ns: resid
id: AA0272
- ns: mod
id: MOD:00277
- ns: pdb.ligand
id: AGM
- ns: pdb-ccd
id: AGM
- ns: go
id: GO:0018181
structure: OC(=O)[C@H](CC[C@@H]([NH+]=C(N)N)C)[NH3+]
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0128:
id: AA0128
name: L-3-phenyllactic acid
synonyms:
- (2S)-2-hydroxy-3-phenylpropanoic acid
- (2S)-2-hydroxy-3-phenyl-propanoic acid
- X
- alpha-hydroxy-beta-phenyl-propionic acid
identifiers:
- ns: resid
id: AA0128
- ns: cas
id: 20312-36-1
- ns: pdb-ccd
id: HFA
- ns: mod
id: MOD:00137
- ns: go
id: GO:0018058
structure: O[C@H](C(=O)O)Cc1ccccc1
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
- molecule: Monomer
element: H
position: 6
AA0592:
id: AA0592
name: 2-(2-aminosuccinimidyl)-3-sulfanylpropanoic acid
comments: 'This cross-link is formed by the condensation of an aspartic acid or
asparagine residue with the alpha-amido of the following residue. Generating
Enzyme: autocatalytic.'
synonyms:
- (2r)-2-[(3s)-3-amino-2,5-dioxopyrrolidin-1-yl]-3-sulfanylpropanoic acid
- DC
- (2R)-2-[(3S)-3-amino-2,5-dioxo-pyrrolidin-1-yl]-3-sulfanyl-propanoic acid
- (2R)-2-[(3S)-3-amino-2,5-dioxopyrrolidin-1-yl]-3-sulfanylpropanoic acid
- aspartimide cysteine
identifiers:
- ns: mod
id: MOD:01939
- ns: mod
id: MOD:01938
- ns: pdb.ligand
id: SIC
- ns: resid
id: AA0592
- ns: pdb-ccd
id: SIC
structure: SC[C@H](N1C(=O)C[C@@H](C1=O)N)C(=O)O
base_monomers:
- N
- D
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
- molecule: Monomer
element: H
position: 16
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
AA0330:
id: AA0330
name: 3-methyl-L-lanthionine sulfoxide
comments: The S-oxide of 3-methyl-L-lanthionine is a chiral center, and the stereoisomer
has not been determined.
synonyms:
- 3-methyl-L-lanthionine S-oxide
- (2S,3S,4Xi,6R)-2,6-diamino-3-methyl-4-oxo-4-thiaheptanedioic acid
- (2S,3S,SXi)-2-amino-3-([(R)-2-amino-2-carboxyethyl]sulfinyl)butanoic acid
- S-oxy-3-methyllanthionine
identifiers:
- ns: mod
id: MOD:00335
- ns: go
id: GO:0046804
- ns: resid
id: AA0330
structure: O=C[C@H](C[S@](=O)[C@H]([C@H](C(=O)O)N)C)N
base_monomers:
- T
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
AA0516:
id: AA0516
name: N-[(12R)-12-hydroxymyristoyl]-L-cysteine
synonyms:
- 2-[(12R)-12-hydroxytetradecanoyl]amino-3-sulfanylpropanoic acid
- N-[(12R)-12-hydroxytetradecanoyl]cysteine
identifiers:
- ns: resid
id: AA0516
- ns: mod
id: MOD:01690
structure: CC[C@H](CCCCCCCCCCC(=O)N[C@H](C(=O)O)CS)O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
AA0365:
id: AA0365
name: (E)-2,3-didehydrotyrosine
synonyms:
- (2E)-2-amino-3-(4-hydroxyphenyl)prop-2-enoic acid
- 4-[(E)-[2-(3-methylsulfanylpropanoyl)-5-oxo-1-(2-oxoethyl)imidazol-4-ylidene]methyl]phenolate
- trans-dehydrotyrosine
- MYG
- para-hydroxybenzylidene-imidazolidinone chromophore
- blue non-fluorescent pocilloporin chromophore
- 4-{(z)-[2-[3-(methylsulfanyl)propanoyl]-5-oxo-1-(2-oxoethyl)-1,5-dihydro-4h-imidazol-4-ylidene]methyl}benzenolate
- 4-[(E)-{2-[3-(methylsulfanyl)propanoyl]-5-oxo-1-(2-oxoethyl)-1,5-dihydro-4H-imidazol-4-ylidene}methyl]phenolate
- amino-(para-hydroxybenzylidenyl)acetic acid
identifiers:
- ns: mod
id: MOD:00370
- ns: pdb-ccd
id: CRK
- ns: resid
id: AA0365
- ns: pdb.ligand
id: CRK
- ns: go
id: GO:0018251
structure: Oc1ccc(cc1)/C=C(\C(=O)O)/N
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
AA0606:
id: AA0606
name: N4-(2,4-diacetamido-2,4,6-trideoxy-D-glucosyl)-L-asparagine
comments: Bacillosamine is a trivial name formed by modification of a non-standard
monosaccharide parent name, and is not recommended by the IUPAC Nomenclature
Committee. Some authors use bacillosamine to refer to the diacetylated form,
rather than the unacetylated form.
synonyms:
- DATDH
- DABA
- DiNAcBac
- (2S)-2-amino-4-[(2,4-diacetylamino-2,4,6-trideoxy-beta-D-glucopyranosyl)amino]-4-oxobutanoic
acid
- N4-[N,N-diacetylbacillosaminyl]asparagine
- N4-[2,4-bis(acetylamino)-2,4,6-trideoxy-beta-D-glucopyranosyl]-L-asparagine
- N4-[N2,N4-diacetylbacillosaminyl]asparagine
identifiers:
- ns: resid
id: AA0606
- ns: mod
id: MOD:01962
- ns: pdb.ligand
id: B6D
structure: O=C(N[C@@H]1O[C@H](C)[C@H]([C@@H]([C@H]1NC(=O)C)O)NC(=O)C)C[C@@H](C(=O)O)N
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 28
l_bond_atoms:
- molecule: Monomer
element: N
position: 31
r_displaced_atoms:
- molecule: Monomer
element: O
position: 30
- molecule: Monomer
element: H
position: 30
l_displaced_atoms:
- molecule: Monomer
element: H
position: 31
AA0204:
id: AA0204
name: S-(2-aminovinyl)-D-cysteine
comments: 'This cross-link arises from the decarboxylation of the carboxyl-terminal
portion of a lanthionine, either L-lanthionine (see RESID:AA0110) or meso-lanthionine
(see RESID:AA0111). This residue is acid labile. It may be identified as (2-aminoethyl)-D-cysteine
(D-4-thialysine) after hydrogenation with palladium/charcoal catalyst. For the
L stereoisomer, see RESID:AA0548. The stereochemistry of the (2-aminovinyl)-cysteine
derived from two L-cysteine residues in cypemycin has not been determined. Generating
Enzyme: peptidyl-cysteine dethiolase (EC 4.4.1.-) #link CYS2; peptidyl-phosphoserine/phosphothreonine
dehydratase (EC 4.2.1.-) #link SER; peptidyl-cysteine dehydroalanine/dehydrobutyrine
ligase (EC 6.2.-.-).'
synonyms:
- (S,Z)-S-(2-aminovinyl)cysteine
- (2S)-2-amino-3-([(Z)-2-aminoethenyl]sulfanyl)propanoic acid
identifiers:
- ns: resid
id: AA0204
- ns: mod
id: MOD:01849
- ns: go
id: GO:0018096
- ns: mod
id: MOD:00209
structure: N/C=C\SC[C@H]([NH3+])C(=O)O
base_monomers:
- S
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
AA0130:
id: AA0130
name: N2-succinyl-L-tryptophan
synonyms:
- (2S)-2-(3-carboxypropanoyl)amino-3-(1H-indol-3-yl)propanoic acid
- (2S)-2-amino-(6,7-dihydro-6,7-dioxo-1H-indole)-3-propanoic acid
identifiers:
- ns: resid
id: AA0130
- ns: go
id: GO:0018062
- ns: mod
id: MOD:00139
- ns: cas
id: 514803-26-0
structure: O=C[C@H](Cc1c[nH]c2c1cccc2)NC(=O)CCC(=O)[O-]
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 21
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
AA0260:
id: AA0260
name: phycourobilin-bis-L-cysteine
comments: There are additional chiral centers at C-3alpha, C-4, C-16 and C-18alpha.
synonyms:
- 3,18-bis(1-[(R)-2-amino-2-carboxyethyl]sulfanylethyl)-8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-4,5,15,16-tetrahydro-(21H,22H,24H)-bilene-b-1,19(4H,16H)-dione
- PUB
- phycourobilin biscysteine adduct
- 3,18-bis(1-[(R)-2-amino-2-carboxyethyl]sulfanylethyl)-2,7,13,17-tetramethyl-1,19-dioxo-4,5,15,16-tetrahydro-(21H,22H,24H)-bilene-b-8,12-dipropanoic
acid
identifiers:
- ns: go
id: GO:0017010
- ns: mod
id: MOD:00265
- ns: cas
id: 61932-71-6
- ns: resid
id: AA0260
- ns: pdb.ligand
id: PUB
structure: O=C[C@H](CS[C@H](C1=C(C)[C@H](NC1=O)Cc1[nH]c(c(c1C)CCC(=O)[O-])Cc1[nH]c(c(c1CCC(=O)[O-])C)C[C@@H]1NC(=O)C(=C1[C@H](SC[C@@H](C=O)[NH3+])C)C)C)[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 27
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
r_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
AA0328:
id: AA0328
name: (3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine
comments: The structure shown has been independently confirmed. Asparagine is
converted to an aspartyl-1-amide by a process requiring two ATP molecules and
the formation of a peptidyl-succinimide intermediate. The phosphorus atom is
a chiral center that has not been resolved.
synonyms:
- 5'-O-[(3-aminopropoxy)(L-aspart-1-ylamino)phosphoryl]adenosine
- microcin C7 asparagine modification
- 9-(5'-O-[(3-aminopropoxy)(L-aspart-1-ylamino)phosphoryl]-beta-D-ribofuranosyl)adenine
- N-(aspart-1-yl)-O-(3-aminopropyl)-O-(5'-adenosyl)phosphoramide
identifiers:
- ns: chebi
id: CHEBI:60869
- ns: go
id: GO:0046550
- ns: resid
id: AA0328
- ns: mod
id: MOD:00333
structure: '[NH3+]CCCO[P@](=O)(NC(=O)[C@H](CC(=O)[O-])N)OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1NC=N[C@@H]2N'
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AA0069:
id: AA0069
name: omega-N-methyl-L-arginine
comments: 'Generating Enzyme: histone-arginine N-methyltransferase (EC 2.1.1.125);
[myelin basic protein]-arginine N-methyltransferase (EC 2.1.1.126).'
synonyms:
- (2S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acid
- NG-methylarginine
identifiers:
- ns: resid
id: AA0069
- ns: cas
id: 17035-90-4
- ns: chebi
id: CHEBI:28229
- ns: go
id: GO:0018216
- ns: mod
id: MOD:00078
structure: CNC(=[NH2])NCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0537:
id: AA0537
name: 3'-nitro-L-tyrosine
comments: This modification is produced artifactually by treatment with peroxynitrite.
synonyms:
- meta-nitro-tyrosine
- (2S)-2-amino-3-(4-hydroxy-3-nitro-phenyl)propanoic acid
- (2S)-2-amino-3-(4-hydroxy-3-nitrophenyl)propanoic acid
- 3-nitrotyrosine
- Y
- m-nitrotyrosine
- 3-nitro-L-tyrosine
- meta-nitrotyrosine
identifiers:
- ns: pdb-ccd
id: NIY
- ns: chebi
id: CHEBI:44454
- ns: mod
id: MOD:01786
- ns: resid
id: AA0537
- ns: pdb.ligand
id: NIY
- ns: cas
id: 3604-79-3
structure: OC(=O)[C@H](Cc1ccc(c(c1)N(=O)=O)[O-])[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
AA0106:
id: AA0106
name: S-palmitoyl-L-cysteine
comments: 'Although the predominant palmitoyl transferase in mammalian systems
appears to utilize a mixture of saturated and unsaturated fatty acids, some
systems may be more specific in their incorporation of other fatty acids. See
RESID:AA0307 and RESID:AA0308. This modification should not be confused with
N-palmitoyl-cysteine (see RESID:AA0060). Generating Enzyme: protein-cysteine
S-palmitoyltransferase (EC 2.3.1.-).'
synonyms:
- 2-amino-3-(hexadecanoylthio)propanoic acid
- cysteine hexadecanoate thioester
- (2R)-2-amino-3-hexadecanoylsulfanyl-propanoic acid
- s-palmitoyl-l-cysteine
- C
- cysteine palmitate thioester
- (2R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid
- S-hexadecanoyl-L-cysteine
identifiers:
- ns: go
id: GO:0018230
- ns: pdb.ligand
id: PLM
- ns: mod
id: MOD:00115
- ns: resid
id: AA0106
- ns: cas
id: 114507-35-6
- ns: pdb-ccd
id: P1L
structure: CCCCCCCCCCCCCCCC(=O)SC[C@@H](C(=O)O)N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 22
l_bond_atoms:
- molecule: Monomer
element: N
position: 25
r_displaced_atoms:
- molecule: Monomer
element: O
position: 24
- molecule: Monomer
element: H
position: 24
l_displaced_atoms:
- molecule: Monomer
element: H
position: 25
AA0522:
id: AA0522
name: O4-(8alpha-FAD)-L-aspartate
comments: 'Generating Enzyme: autocatalytic.'
synonyms:
- 8alpha-[(4-aspartyl)oxy]FAD
- (2S)-2-amino-4-oxo-4-[8alpha-riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester
with adenosine]oxybutanoic acid
identifiers:
- ns: resid
id: AA0522
- ns: pdb.ligand
id: FAD
- ns: mod
id: MOD:01668
structure: O=C(C[C@@H](C(=O)O)[NH3+])OC[C@@H]1C=c2c(C=C1C)nc1c(n2C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O[P@](=O)(OC[C@H]2O[C@H]([C@@H]([C@@H]2O)O)n2cnc3c2NC=N[C@H]3N)[O-])[O-])O)O)O)[nH]c(=O)[nH]c1=O
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
- molecule: Monomer
element: H
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
G, N:
id: AA0441
name: (2-aminosuccinimidyl)acetic acid
comments: 'This cross-link is formed by the condensation of an aspartic acid or
asparagine residue with the alpha-amido of the following residue. Generating
Enzyme: autocatalytic.'
synonyms:
- anhydroaspartyl glycine
- (3-amino-2,5-dioxo-1-pyrrolidinyl)acetic acid
- aspartimide glycine
- '[(3S)-3-amino-2,5-dioxopyrrolidin-1-yl]acetic acid'
- N-(2-aminosuccinyl)glycine
identifiers:
- ns: mod
id: MOD:01624
- ns: mod
id: MOD:00952
- ns: resid
id: AA0441
- ns: pdb.ligand
id: ACY
- ns: chebi
id: CHEBI:45890
structure: OC(=O)CN1C(=O)C[C@@H](C1=O)N
base_monomers:
- N
- D
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
AA0463:
id: AA0463
name: 3-hydroxy-L-valine
synonyms:
- V
- (2S)-2-amino-3-hydroxy-3-methyl-butanoic acid
- 3-hydroxyvaline
- 3-hydroxy-l-valine
- 3-hydroxy-L-valine
- (2S)-2-amino-3-hydroxy-3-methylbutanoic acid
identifiers:
- ns: mod
id: MOD:01386
- ns: resid
id: AA0463
- ns: pdb-ccd
id: HVA
structure: OC(=O)[C@H](C(O)(C)C)[NH3+]
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
AA0262:
id: AA0262
name: L-cysteine sulfinic acid
synonyms:
- 3-sulfinoalanine
- cysteine-S,S-dioxide [tautomer]
- (2R)-2-azanyl-3-[(S)-oxidanylsulfinyl]propanoic acid
- S-sulfinocysteine
- (2R)-2-amino-3-sulfinopropanoic acid
- 3-sulphinoalanine
- C
- cysteine sulphinic acid
- 2-amino-3-(dioxido-lambda(6)-sulfanyl)propanoic acid [tautomer]
- 2-amino-2-carboxyethanesulfinic acid
- 2-amino-3-sulfonylpropanoic acid [tautomer]
- 3-sulfino-L-alanine
- S-cysteinesulfinic acid
identifiers:
- ns: go
id: GO:0018171
- ns: mod
id: MOD:00267
- ns: chebi
id: CHEBI:61964
- ns: pdb.ligand
id: CSD
- ns: cas
id: 1115-65-7
- ns: resid
id: AA0262
- ns: pdb-ccd
id: CSD
structure: O[S](C[C@@H](C(=O)O)N)O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
- molecule: Monomer
element: H
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
AA0387:
id: AA0387
name: O-decanoyl-L-threonine
comments: 'Generating Enzyme: ghrelin O-acyltransferase, GOAT (EC 2.3.1.-).'
synonyms:
- (2S)-2-amino-3-(decanoyloxy)propanoic acid
- O3-decanoyl-L-threonine
- L-threonine decanoate ester
identifiers:
- ns: resid
id: AA0387
- ns: mod
id: MOD:00392
- ns: go
id: GO:0042050
structure: CCCCCCCCCC(=O)O[C@@H]([C@@H](C(=O)O)[NH3+])C
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
- molecule: Monomer
element: H
position: 19
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
C, W:
id: AA0313
name: 4'-(S-L-cysteinyl)-L-tryptophyl quinone
synonyms:
- 3-(2-amino-2-carboxyethyl)-4-[2-amino-2-carboxyethyl]sulfanyl-6,7-indolinedione
- cysteine tryptophylquinone
- 4-(S-cysteinyl)tryptophan-6,7-dione
- (2R)-2-amino-3-[(3-[(2S)-2-amino-2-carboxyethyl]-6,7-dioxo-6,7-dihydro-1H-indol-4-yl)sulfanyl]propanoic
acid
- CTQ
identifiers:
- ns: resid
id: AA0313
- ns: go
id: GO:0019927
- ns: mod
id: MOD:00318
structure: O=C[C@H](CSC1=CC(=O)C(=O)c2c1c(c[nH]2)C[C@@H](C(=O)O)[NH3+])[NH3+]
base_monomers:
- W
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 22
l_bond_atoms:
- molecule: Monomer
element: N
position: 25
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 24
- molecule: Monomer
element: H
position: 24
l_displaced_atoms:
- molecule: Monomer
element: H
position: 25
- molecule: Monomer
element: H
position: 25
charge: 1
C, F:
id: AA0243
name: L-phenylalanine thiazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-cysteine
cyclase (EC 4.2.1.-); peptidyl-thiazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-[(1S)-1-amino-2-phenylethyl]-1,3-thiazole-4-carboxylic acid
- 2-[1-azanyl-2-phenylethyl]-1,3-thiazole-4-carboxylic acid
identifiers:
- ns: go
id: GO:0018139
- ns: pdb.ligand
id: BB9
- ns: resid
id: AA0243
- ns: mod
id: MOD:00248
structure: OC(=O)c1csc(n1)[C@H](Cc1ccccc1)[NH3+]
base_monomers:
- F
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
AA0146:
id: AA0146
name: L-3',4'-dihydroxyphenylalanine
synonyms:
- L-DOPA
- (2S)-2-azanyl-3-[3,4-bis(oxidanyl)phenyl]propanoic acid
- F
- L-3'-hydroxytyrosine
- (2S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid
- 3-hydroxy-L-tyrosine
- levodopa
- 3,4-dihydroxyphenylalanine
identifiers:
- ns: pdb-ccd
id: DAH
- ns: go
id: GO:0018067
- ns: mod
id: MOD:00155
- ns: resid
id: AA0146
- ns: pdb.ligand
id: DAH
- ns: cas
id: 59-92-7
structure: OC(=O)[C@H](Cc1ccc(c(c1)O)O)[NH3+]
base_monomers:
- F
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0244:
id: AA0244
name: L-cysteine thiazole-4-carboxylic acid
comments: "Formed by the condensation of a cysteine thiol with the carbonyl of\
\ the preceding residue and alpha-beta dehydrogenation. The first cysteine may\
\ be condensed on the carbonyl of the residue preceding it, forming a 2,4'-bithiazole\
\ structure. Generating Enzyme: peptidyl-cysteine cyclase (EC 4.2.1.-); peptidyl-thiazoline\
\ dehydrogenase (EC 1.3.-.-)."
synonyms:
- 2-[1-azanyl-2-sulfanylethyl]-1,3-thiazole-4-carboxylic acid
- 2-[(1S)-1-amino-2-sulfanylethyl]-1,3-thiazole-4-carboxylic acid
identifiers:
- ns: resid
id: AA0244
- ns: pdb.ligand
id: BB9
- ns: mod
id: MOD:00249
- ns: go
id: GO:0018140
structure: OC(=O)c1csc(n1)[C@@H]([NH3+])CS
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
AA0503:
id: AA0503
name: 5-glutamyl 2-aminoadipic 6-phosphoric anhydride
comments: 'Generating Enzyme: LysW-L-glutamate/LysW-L-2-aminoadipate kinase, LysZ
(EC 2.7.2.-).'
synonyms:
- (2S)-2-([(4S)-4-amino-4-carboxybutanoyl]amino)-6-oxo-6-(phosphonooxy)hexanoic
acid
identifiers:
- ns: resid
id: AA0503
- ns: mod
id: MOD:01606
structure: O=C[C@H](CCC(=O)N[C@H](C(=O)[O-])CCCC(=O)OP(=O)([O-])[O-])[NH3+]
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
C, S, S:
id: AA0470
name: L-cysteine pyridine-2,5-dicarboxylic acid
comments: Formed by the metathesis of two didehydroalanines made from serines,
condensation with a cysteine carbonyl and dehydrogenation. This modification
is currently represented in the PDB as part of the HET group for the entire
molecule of antibiotic GE2270 A.
synonyms:
- 6-[(1R)-1-amino-2-sulfanylethyl]pyridine-2,5-dicarboxylic acid
identifiers:
- ns: resid
id: AA0470
- ns: mod
id: MOD:01393
- ns: pdb.ligand
id: GEA
structure: SC[C@@H](c1nc(ccc1C=O)C(=O)O)[NH3+]
base_monomers:
- S
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
AA0518:
id: AA0518
name: N5-(ADP-ribosyl)-L-glutamine
comments: 'It is not known whether Photorhabdus luminescens toxin catalyzes formation
of the alpha or beta isomer. The alpha form is presented. The keyword "phosphoprotein"
is not used with toxin modification. Generating Enzyme: NAD(P)+--glutamine ADP-ribosyltransferase
TccC5 (EC 2.4.2.-).'
synonyms:
- N5-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-glutamine
- (S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-5-oxopentanoic
acid
- N5-alpha-D-ribofuranosyl-L-glutamine 5'->5'-ester with adenosine 5'-(trihydrogen
diphosphate)
identifiers:
- ns: resid
id: AA0518
- ns: mod
id: MOD:01662
structure: O=C(N[C@H]1O[C@H]([C@H]([C@H]1O)O)CO[P@@](=O)(O[P@](=O)(OC[C@@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1NC=N[C@H]2N)[O-])[O-])CC[C@@H](C(=O)O)[NH3+]
base_monomers:
- Q
r_bond_atoms:
- molecule: Monomer
element: C
position: 52
l_bond_atoms:
- molecule: Monomer
element: N
position: 55
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 54
- molecule: Monomer
element: H
position: 54
l_displaced_atoms:
- molecule: Monomer
element: H
position: 55
- molecule: Monomer
element: H
position: 55
charge: 1
AA0389:
id: AA0389
name: O4-galactosyl-L-hydroxyproline
comments: See also RESID:AA0212 and RESID:AA0390 for other O4-glycosylated 4-hydroxyprolines.
synonyms:
- (2S,4R)-4-(beta-D-galactopyranosyloxy)pyrrolidine-2-carboxylic acid
- 4-(beta-D-galactopyranosyloxy)proline
- 4-(galactosyloxy)proline
- beta-galactopyranosyl-4-hydroxyproline
- O4-glycosyl-hydroxyproline
identifiers:
- ns: mod
id: MOD:00757
- ns: resid
id: AA0389
structure: OC[C@H]1O[C@@H](O[C@H]2C[NH2+][C@@H](C2)C(=O)O)[C@@H]([C@H]([C@H]1O)O)O
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
- molecule: Monomer
element: H
position: 20
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
AA0154:
id: AA0154
name: O-(N-acetylaminogalactosyl)-L-serine
comments: 'See also RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291, RESID:AA0296,
RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402, RESID:AA0404,
RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines. Generating
Enzyme: polypeptide N-acetylgalactosaminyltransferase (EC 2.4.1.41).'
synonyms:
- O3-(N-acetylgalactosaminyl)serine
- (2S)-2-amino-3-(2-acetamido-2-deoxy-alpha-D-galactopyranosyloxy)propanoic acid
- mucin type O-glycosylserine
identifiers:
- ns: go
id: GO:0006493
- ns: resid
id: AA0154
- ns: mod
id: MOD:00163
- ns: chebi
id: CHEBI:53604
structure: OC[C@H]1O[C@@H](OC[C@@H](C(=O)O)[NH3+])[C@@H]([C@H]([C@H]1O)O)NC(=O)C
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0259:
id: AA0259
name: phycoerythrobilin-bis-L-cysteine
comments: There are additional chiral centers at C-2, C-3, and C-16. The phytochromobilins
and phycoerythrobilins transmit red.
synonyms:
- PEB
- (2S,3R,16R)-3,18-bis-[(R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-2,3,15,16-tetrahydrobilin-1,19(21H,22H,24H)-dione
- 3,18-bis-[1-((2-amino-2-carboxy)ethylsulfanyl)ethyl]-2,3,15,16-tetrahydro-2,7,13,17-tetramethyl-1,19-dioxo-(21H,22H,24H)-biladiene-ab-8,12-dipropanoic
acid
- phycoerythrobilin biscysteine adduct
identifiers:
- ns: go
id: GO:0017011
- ns: resid
id: AA0259
- ns: mod
id: MOD:00264
- ns: cas
id: 18097-67-1
structure: O=C[C@H](CS[C@@H]([C@H]1/C(=C/[C@@H]2[NH2+]/C(=C\c3[nH]c(c(c3CCC(=O)[O-])C)C[C@H]3NC(=O)C(=C3C)[C@@H](SC[C@@H](C=O)[NH3+])C)/C(=C2C)CCC(=O)[O-])/NC(=O)[C@H]1C)C)[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 28
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0081:
id: AA0081
name: L-alanine amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- (2S)-2-aminopropanamide
- alaninamide
identifiers:
- ns: resid
id: AA0081
- ns: go
id: GO:0018034
- ns: chebi
id: CHEBI:21217
- ns: mod
id: MOD:00090
- ns: pdb.ligand
id: NH2
- ns: cas
id: 7324-05-2
structure: C[C@H]([NH3+])C(=O)N
base_monomers:
- A
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
- molecule: Monomer
element: H
position: 4
charge: 1
AA0370:
id: AA0370
name: 4,5-dihydroxy-L-lysine
comments: Hydroxylations at C-4 and C-5 are assumed. Neither the positions of
the hydroxylations nor the stereochemistry for the chiral centers they produce
have been determined. The (2S,4R,5R) stereoisomer is shown.
synonyms:
- alpha,epsilon-diamino-delta,gamma-dihydroxycaproic acid
- (2S,4Xi,5Xi)-2,6-diamino-4,5-dihydroxyhexanoic acid
- delta,gamma-dihydroxylysine
identifiers:
- ns: resid
id: AA0370
- ns: mod
id: MOD:00375
- ns: go
id: GO:0030963
structure: '[NH3+]C[C@H]([C@@H](C[C@@H](C(=O)O)[NH3+])O)O'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0264:
id: AA0264
name: O-(sn-1-glycerophosphoryl)-L-serine
comments: The stereochemistry of the glycerol phosphate has not been determined.
The sn-1 form is assumed.
synonyms:
- O3-(sn-1-glycerophosphoryl)-L-serine
- alpha-glycerophosphoryl serine
- O3-2,3-dihydroxypropyl hydrogen phosphate-L-serine ester
- glycerophosphoserine
- (2S)-2-amino-3-[(2Xi)-2,3-dihydroxypropyl]phosphonoxypropanoic acid
- O3-L-serine glyceryl-1-phosphodiester
identifiers:
- ns: go
id: GO:0018340
- ns: pdb.ligand
id: OPE
- ns: resid
id: AA0264
- ns: cas
id: 26289-09-8
- ns: mod
id: MOD:00269
structure: OC[C@@H](COP(=O)(OC[C@@H](C(=O)O)[NH3+])[O-])O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0039:
id: AA0039
name: O4'-phospho-L-tyrosine
comments: 'Generating Enzyme: protein-tyrosine kinase (EC 2.7.1.112).'
synonyms:
- O4-phosphotyrosine
- (2S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid
- o-phosphotyrosine
- tyrosine phosphate
- 2-azanyl-3-(4-phosphonooxyphenyl)propanoic acid
- O-phosphono-L-tyrosine
- 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate
- Y
identifiers:
- ns: pdb-ccd
id: PTR
- ns: resid
id: AA0039
- ns: chebi
id: CHEBI:61972
- ns: mod
id: MOD:00048
- ns: pdb.ligand
id: PTR
- ns: go
id: GO:0018108
- ns: cas
id: 21820-51-9
structure: OC(=O)[C@H](Cc1ccc(cc1)OP(=O)([O-])[O-])[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0152:
id: AA0152
name: S-glucosyl-L-cysteine
comments: The beta anomeric form is shown. See also RESID:AA0392 and RESID:AA0560
for other S-glycosylated cysteines.
synonyms:
- S-(beta-D-glucopyranosyl)cysteine
- (2R)-2-amino-3-[(beta-D-glucopyranosyl)sulfanyl]propanoic acid
- S-glycosyl-cysteine
identifiers:
- ns: resid
id: AA0152
- ns: go
id: GO:0018240
- ns: mod
id: MOD:00161
structure: OC[C@H]1O[C@@H](SC[C@@H](C(=O)O)[NH3+])[C@@H]([C@H]([C@@H]1O)O)O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0096:
id: AA0096
name: L-serine amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- serinamide
- aminoserine
- (2S)-2-amino-3-hydroxypropanamide
- S
- (2S)-2-amino-3-hydroxy-propanamide
- L-serinamide
identifiers:
- ns: pdb-ccd
id: SET
- ns: chebi
id: CHEBI:21389
- ns: resid
id: AA0096
- ns: mod
id: MOD:00105
- ns: cas
id: 6791-49-7
- ns: go
id: GO:0018049
- ns: pdb.ligand
id: NH2
structure: NC(=O)[C@@H]([NH3+])CO
base_monomers:
- S
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0242:
id: AA0242
name: L-serine thiazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-cysteine
cyclase (EC 4.2.1.-); peptidyl-thiazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-[(1S)-1-amino-2-hydroxyethyl]-1,3-thiazole-4-carboxylic acid
- 2-[1-azanyl-2-hydroxyethyl]-1,3-thiazole-4-carboxylic acid
identifiers:
- ns: go
id: GO:0018138
- ns: pdb.ligand
id: BB9
- ns: mod
id: MOD:00247
- ns: resid
id: AA0242
structure: OC[C@@H](c1scc(n1)C(=O)O)[NH3+]
base_monomers:
- S
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
AA0563:
id: AA0563
name: L-cysteine bacillithiol disulfide
comments: 'Generating Enzyme: autocatalytic.'
synonyms:
- BSH
- (2S)-(2-[S-(L-cystein-S-yl)-L-cysteinyl]amino-2-deoxy-alpha-D-glucopyranosyloxy)-butanedioic
acid
identifiers:
- ns: chebi
id: CHEBI:61338
- ns: mod
id: MOD:01860
- ns: resid
id: AA0563
structure: O=C[C@H](CSSC[C@@H](C(=O)N[C@@H]1[C@@H](O[C@@H]([C@H]([C@H]1O)O)CO)O[C@H](C(=O)[O-])CC(=O)[O-])[NH3+])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 32
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 34
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
AA0380:
id: AA0380
name: L-asparagine 5-imidazolinone glycine
comments: 'This entry represents the cross-link of the peptide backbone from the
alpha-carboxyl carbon of residue N, an asparagine, to the alpha-amino nitrogen
of residue N+2, a glycine, coupled with the formation of a double bond to the
alpha-amino nitrogen of residue N+1 which loses one hydrogen, and the loss of
a molecule of water. This cross-link is accompanied by modification of residue
N+1. The modified residue N+1 is presented in a separate entry and is not included
in the mass accounting of this entry. The backbone atoms of residue N+1 are
shown in gray in the diagram. Generating Enzyme: autocatalytic.'
synonyms:
- (2-[(1S)-1,3-diamino-3-oxopropyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl)acetic
acid
- 2-[(4Z)-2-[(1S)-1,3-diamino-3-oxo-propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-imidazol-1-yl]ethanoic
acid
- '{(4Z)-2-[(1S)-1,3-diamino-3-oxopropyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid'
- asparaginyl-5-imidazolinone glycine
- '[(4z)-2-[(1s)-1,3-diamino-3-oxopropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic
acid'
- NYG
- '[2-(1,3-diamino-3-oxopropyl)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid'
- Zoanthus sp. fluorescent protein FP506 chromophore
- para-hydroxybenzylidene-imidazolidinone chromophore
- 2-[(S)-1,3-diamino-3-oxopropyl]-1-carboxymethyl-1-imidazolin-5-one
identifiers:
- ns: mod
id: MOD:00385
- ns: pdb-ccd
id: NYG
- ns: resid
id: AA0380
- ns: pdb.ligand
id: NYG
- ns: go
id: GO:0051360
structure: NC(=O)C[C@@H](C1=NCC(=O)N1CC(=O)O)N
base_monomers:
- N
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
- molecule: Monomer
element: H
position: 16
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0074:
id: AA0074
name: N6,N6,N6-trimethyl-L-lysine
comments: 'Consult FAQ at http://pir.georgetown.edu/resid/faq.shtml#q12 concerning
calculation of the difference formula. Generating Enzyme: histone-lysine N-methyltransferase
(EC 2.1.1.43); cytochrome-c-lysine N-methyltransferase (EC 2.1.1.59); calmodulin-lysine
N-methyltransferase (EC 2.1.1.60).'
synonyms:
- N(zeta)-trimethyllysine
- 5-azanyl-5-carboxy-N,N,N-trimethylpentanazanium
- N-[(5S)-5-amino-5-carboxypentyl]-N,N-dimethylmethanaminium
- K
- 2-amino-6-(trimethylammonio)hexanoic acid
- epsilon-trimethyllysine
- N6,N6,N6-trimethyllysine cation
- n-trimethyllysine
- N6,N6,N6-trimethyllysin-N6-ium
- (5S)-5-amino-5-carboxy-N,N,N-trimethylpentan-1-aminium
- '[(5S)-5-amino-6-hydroxy-6-oxo-hexyl]-trimethyl-azanium'
identifiers:
- ns: resid
id: AA0074
- ns: chebi
id: CHEBI:61961
- ns: pdb-ccd
id: M3L
- ns: cas
id: 19253-88-4
- ns: go
id: GO:0018023
- ns: pdb.ligand
id: M3L
- ns: mod
id: MOD:00083
structure: OC(=O)[C@H](CCCC[N](C)(C)C)N
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
AA0524:
id: AA0524
name: N6-chloro-L-lysine
comments: 'In tryptophan 7-halogenase (EC 1.14.14.7), the modification is formed
by autocatalysis as an intermediate in the catalytic cycle. The formation by
myeloperoxidase (EC 1.11.1.7) is probably not a normal metabolic process. Generating
Enzyme: autocatalytic; myeloperoxidase (EC 1.11.1.7).'
synonyms:
- lysine chloramine
- N(zeta)-chlorolysine
- (2S)-2-amino-6-(chloroamino)hexanoic acid
- epsilon-chlorolysine
identifiers:
- ns: mod
id: MOD:01670
- ns: resid
id: AA0524
structure: ClNCCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
- molecule: Monomer
element: H
position: 11
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
AA0205:
id: AA0205
name: L-cysteine sulfenic acid
comments: This reactive residue must be stabilized by the protein structure. As
a active site it may be reduced to cysteine or cysteine anion and reoxidized
during the reaction cycle. The "active site" feature is used if the stable form
is the reduced cysteine; the "modified site" feature is used if the stable form
is the oxidized cysteine sulfenic acid.
synonyms:
- S-hydroxycysteine
- 3-sulfenoalanine
- (2R)-2-amino-3-hydroxysulfanyl-propanoic acid
- 2-amino-3-sulfinylpropanoic acid [tautomer]
- 2-amino-2-carboxyethanesulfenic acid
- S-oxocysteine [tautomer]
- (2R)-2-amino-3-(oxido-lambda(4)-sulfanyl)propanoic acid [tautomer]
- cysteine S-oxide [tautomer]
- C
- S-oxycysteine [tautomer]
- (2R)-2-amino-3-(hydroxysulfanyl)propanoic acid
- S-hydroxy-L-cysteine
- s-hydroxycysteine
- cysteine sulfoxide [tautomer]
- cysteine sulphenic acid
identifiers:
- ns: resid
id: AA0205
- ns: go
id: GO:0018171
- ns: chebi
id: CHEBI:61962
- ns: cas
id: 5722-80-5
- ns: mod
id: MOD:00210
- ns: pdb.ligand
id: CSO
- ns: pdb-ccd
id: CSO
structure: OSC[C@@H](C(=O)O)[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
- molecule: Monomer
element: H
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
AA0216:
id: AA0216
name: N-(L-isoaspartyl)-L-cysteine
synonyms:
- (S)-2-amino-4-((R)-1-carboxy-2-sulfanylethyl)amino-4-oxobutanoic acid
- N-isoaspartyl cysteine
- 2-(3-amino-3-carboxypropanoyl)amino-3-mercaptopropanoic acid
- N-beta-aspartylcysteine
- 2-amino-N4-(1-carboxy-2-mercaptoethyl)butanediamic acid
identifiers:
- ns: mod
id: MOD:00221
- ns: go
id: GO:0018263
- ns: resid
id: AA0216
structure: SC[C@@H](C(=O)O)NC(=O)C[C@@H](C=O)N
base_monomers:
- N
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
- molecule: Monomer
element: H
position: 7
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
AA0556:
id: AA0556
name: L-cysteine sulfonic acid
comments: This modification is easily produced artifactually. Cysteine sulfinic
acid (see RESID:AA0262) exposed to air oxidizes to cysteic acid.
synonyms:
- 2-amino-2-carboxyethanesulfonic acid
- (2R)-2-azanyl-3-sulfo-propanoic acid
- (2R)-2-amino-3-sulfopropanoic acid
- 3-sulfoalanine
- 3-sulfo-L-alanine
- C
- cysteine sulphonic acid
- 2-azanyl-3-sulfopropanoic acid
- cysteic acid
- cysteinesulfonic acid
identifiers:
- ns: cas
id: 498-40-8
- ns: resid
id: AA0556
- ns: chebi
id: CHEBI:17285
- ns: pdb-ccd
id: OCS
- ns: pdb.ligand
id: OCS
- ns: mod
id: MOD:00460
structure: OC(=O)[C@H](CS(O)(O)O)N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
K, K, K, K:
id: AA0588
name: Isodesmosine
comments: 'After the oxidation of three of the four lysines to allysine (see RESID:AA0121),
this cross-link forms spontaneously with a Schiff-base reaction, and a series
of one aldimine and two aldol condensation reactions. In this aleatoric modification
up to four peptide chains may be crosslinked, with each peptide contributing
a lysine potentially in any of the four biosynthetic positions. Desmosine is
a structural isomer (see RESID:AA0587). Up to two of the lysines forming the
cross-link may also be hydroxylated and glycosylated (see RESID:AA0028 and RESID:AA0153).
Generating Enzyme: lysyl oxidase (EC 1.4.3.13).'
synonyms:
- 6-[2-(4-amino-4-carboxybutyl)-3,5-bis(3-amino-3-carboxypropyl)pyridinio]norleucine
- 2-[(4S)-4-amino-4-carboxybutyl]-1-[(5S)-5-amino-5-carboxypentyl]-3,5-bis[(3S)-3-amino-3-carboxypropyl]pyridinium
identifiers:
- ns: chebi
id: CHEBI:64366
- ns: cas
id: 991-01-5
- ns: mod
id: MOD:01934
- ns: resid
id: AA0588
structure: O=C[C@H](CCCC[NH+]1C=C(CC[C@@H](C(=O)O)[NH3+])CC(=C1CCC[C@@H](C=O)[NH3+])CC[C@@H](C=O)[NH3+])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
- molecule: Monomer
element: H
position: 19
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
AA0446:
id: AA0446
name: (2S,4S)-4,5-dihydroxyleucine
synonyms:
- (2s,4s)-2-amino-4,5-dihydroxy-4-methylpentanoic acid
- (2S,4S)-2-amino-4,5-dihydroxy-4-methylpentanoic acid (non-preferred name)
- gamma,delta-dihydroxyleucine
- (2~{S},4~{S})-2-azanyl-4-methyl-4,5-bis(oxidanyl)pentanoic acid
- (4S)-4,5-dihydroxyleucine
- (2S,4S)-2-amino-4,5-dihydroxy-4-methylpentanoic acid
identifiers:
- ns: pdb-ccd
id: G5G
- ns: mod
id: MOD:01432
- ns: resid
id: AA0446
structure: OC[C@](C[C@@H](C(=O)O)[NH3+])(O)C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
AA0589:
id: AA0589
name: O-glucosyl-L-hydroxylysine
comments: 'The mimivirus enzyme is bifunctional and carries out both hydroxylation
and glucosylation. Neither the regiospecificity nor stereospecificity of the
hydroxylation, nor the anomeric specificity of the glucosylation have been determined.
The 5-hydroxy, beta anomeric form is shown. Generating Enzyme: lysine dioxygenase
(EC 1.14.11.-); hydroxylysine glucosyltransferase (EC 2.4.1.-).'
synonyms:
- (D-glucopyranosyl)oxy-L-lysine
identifiers:
- ns: mod
id: MOD:01935
- ns: resid
id: AA0589
structure: OC[C@H]1O[C@@H](O[C@H](CC[C@@H](C(=O)O)[NH3+])C[NH3+])[C@@H]([C@H]([C@@H]1O)O)O
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
- molecule: Monomer
element: H
position: 17
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
G, M:
id: AA0379
name: 2-imino-methionine 5-imidazolinone glycine
comments: 'This entry represents the cross-link of the peptide backbone from the
alpha-carboxyl carbon of residue N, a methionine, to the alpha-amino nitrogen
of residue N+2, a glycine, coupled with the formation of a double bond to the
alpha-amino nitrogen of residue N, and the loss of a molecule of water. This
cross-link is accompanied by modification of residue N+1. The modified residue
N+1 is presented in a separate entry and is not included in the mass accounting
of this entry. The backbone atoms of residue N+1 are shown in gray in the diagram.
In the asFP595 chromoprotein, the peptide chain is cleaved at the methionine
alpha-amino. For a previously proposed structure of the asFP595 chromoprotein,
see RESID:AA0377. Generating Enzyme: autocatalytic.'
synonyms:
- 2,N-didehydromethionyl-5-imidazolinone glycine
- 2-[1-imino-3-(methylsulfanyl)propyl]-1-carboxymethyl-1-imidazolin-5-one
- GFP-like chromoprotein asFP595 chromophore
- (2-[3-(methylsulfanyl)propanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl)acetic
acid
- MYG
- 2-[(4Z)-4-[(4-hydroxyphenyl)methylidene]-2-(3-methylsulfanylpropanimidoyl)-5-oxo-imidazol-1-yl]ethanoic
acid
- para-hydroxybenzylidene-imidazolidinone chromophore
- red fluorescent protein eqFP611 chromophore
- '{(4Z)-4-[(4-hydroxyphenyl)methylidene]-2-[(1Z)-3-(methylsulfanyl)propanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid'
- '{(4z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio)propanimidoyl]-5-oxo-4,5-dihydro-1h-imidazol-1-yl}acetic
acid'
- (2-[1-imino-3-(methylsulfanyl)propyl]-5-oxo-4,5-dihydro-imidazol-1-yl)acetic
acid
- 2-imino-methionyl-5-imidazolinone glycine
identifiers:
- ns: go
id: GO:0051359
- ns: mod
id: MOD:00384
- ns: pdb.ligand
id: NRQ
- ns: pdb-ccd
id: NRQ
- ns: resid
id: AA0379
structure: CSCCC(=N)C1=NCC(=O)N1CC(=O)O
base_monomers:
- M
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
- molecule: Monomer
element: H
position: 16
AA0033:
id: AA0033
name: L-aspartic 4-phosphoric anhydride
synonyms:
- 2-aminobutanedioic 4-phosphoric anhydride
- D
- 4-oxo-O-phosphono-L-homoserine
- 2-azanyl-4-oxo-4-(phosphonooxy)butanoic acid
- 4-phosphoaspartic acid
- aspartyl phosphate
- beta-aspartyl phosphate
- (2S)-2-amino-4-oxo-4-phosphonooxy-butanoic acid
- (2S)-2-amino-4-oxo-4-(phosphonooxy)butanoic acid
identifiers:
- ns: mod
id: MOD:00042
- ns: go
id: GO:0018443
- ns: pdb-ccd
id: PHD
- ns: resid
id: AA0033
- ns: cas
id: 22138-53-0
- ns: pdb.ligand
id: PHD
- ns: chebi
id: CHEBI:15836
structure: O=C(OP(=O)([O-])[O-])C[C@@H](C(=O)O)[NH3+]
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
AA0403:
id: AA0403
name: O-mannosyl-L-threonine
comments: 'See also RESID:AA0155, RESID:AA0247, RESID:AA0399, RESID:AA0401, RESID:AA0405,
and RESID:AA0515 for other O-glycosylated threonines. Generating Enzyme: dolichyl-phosphate-mannose-protein
mannosyltransferase (EC 2.4.1.109).'
synonyms:
- O-glycosylthreonine
- O3-mannosylthreonine
- (2S,3R)-2-amino-3-(alpha-D-mannopyranosyloxy)butanoic acid
identifiers:
- ns: resid
id: AA0403
- ns: mod
id: MOD:00811
structure: OC[C@H]1O[C@H](O[C@@H]([C@@H](C(=O)O)[NH3+])C)[C@H]([C@H]([C@@H]1O)O)O
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0398:
id: AA0398
name: O-(N-acetylamino)glucosyl-L-serine
comments: 'See also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291,
RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0400, RESID:AA0402, RESID:AA0404,
RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines. Generating
Enzyme: [protein]-L-serine/L-threonine beta-N-acetyl-D-glucosaminyl-transferase
(EC 2.4.1.-).'
synonyms:
- (2S)-2-amino-3-(2-acetamido-2-deoxy-beta-D-glucopyranosyloxy)propanoic acid
- O3-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-L-serine
- O-(N-acetylglucosaminyl)serine
- O3-(N-acetylglucosaminyl)serine
- O-(2-acetylamino-2-deoxy-beta-D-glucopyranosyl)-L-serine
- O-glycosylserine
- O-seryl-beta-N-acetylglucosaminide
identifiers:
- ns: pdb.ligand
id: NAG
- ns: mod
id: MOD:00805
- ns: cas
id: 10036-64-3
- ns: resid
id: AA0398
structure: OC[C@H]1O[C@@H](OC[C@@H](C(=O)O)[NH3+])[C@@H]([C@H]([C@@H]1O)O)NC(=O)C
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0465:
id: AA0465
name: 1-amino-2-propanol
synonyms:
- 2-hydroxy-1-propylamine
- (2R)-1-aminopropan-2-ol
- alpha-aminoisopropyl alcohol
- 1-methyl-2-aminoethanol
- decarboxylated threonine
- 2-amino-1-methylethanol
- isopropanolamine
- 1-amino-2-hydroxypropane
- 2-hydroxypropanamine
- 2-hydroxypropylamine
- threamine
identifiers:
- ns: cas
id: 35320-23-1
- ns: mod
id: MOD:01388
- ns: chebi
id: CHEBI:15675
- ns: resid
id: AA0465
structure: C[C@H](C[NH3+])O
base_monomers:
- T
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
AA0549:
id: AA0549
name: 5'-chloro-L-tryptophan
synonyms:
- (2S)-2-amino-3-(5-chloro-1H-indol-3-yl)propanoic acid
identifiers:
- ns: resid
id: AA0549
- ns: mod
id: MOD:01843
- ns: cas
id: 33468-35-8
structure: OC(=O)[C@@H]([NH3+])Cc1c[nH]c2c1cc(Cl)cc2
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
AA0612:
id: AA0612
name: 5-glutamyl N2-glutamate
comments: 'This entry is for isoglutamyl glutamic acid where there is a single
glutamic acid attached to a peptide glutamyl residue by an isopeptide bond.
For L-isoglutamyl-polyglutamic acid where there are 2 to 6 alpha-peptide linked
glutamic acid residues attached to a peptide glutamyl residue by an isopeptide
bond, see RESID:AA0202. Generating Enzyme: glutamate--LysW ligase, ArgX (EC
6.3.2.-).'
synonyms:
- gamma-glutamylglutamate
- 2-([4-azanyl-4-carboxybutanoyl]azanyl)pentanedioic acid
- (2S)-2-[(4S)-4-amino-4-carboxybutanamido]pentanedioic acid
- isoglutamyl glutamic acid
- (2S)-2-([(4S)-4-amino-4-carboxybutanoyl]amino)pentanedioic acid
- isoglutamyl monoglutamic acid
- N-(gamma-L-glutamyl)-L-glutamic acid
identifiers:
- ns: resid
id: AA0612
- ns: cas
id: 1116-22-9
- ns: mod
id: MOD:01970
structure: O=C[C@H](CCC(=O)N[C@H](C(=O)[O-])CCC(=O)[O-])[NH3+]
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
AA0230:
id: AA0230
name: S-nitrosyl-L-cysteine
comments: 'The reaction of nitrosonium (NO+) with cysteine residues may not be
enzymatically catalyzed; the reaction of a cysteine residue with, or the reductive
production of, nitric oxide (NO) has not been clarified. Generating Enzyme:
autocatalytic; peptidyl-cysteine S-nitrosyltransferase (EC 2.6.99.-).'
synonyms:
- (2R)-2-amino-3-nitrososulfanyl-propanoic acid
- s-nitroso-cysteine
- C
- S-nitrosocysteine
- S-nitroso-L-cysteine
- L-cysteine nitrite ester
identifiers:
- ns: pdb-ccd
id: SNC
- ns: mod
id: MOD:00235
- ns: resid
id: AA0230
- ns: cas
id: 51209-75-7
- ns: go
id: GO:0018119
structure: O=NSC[C@@H](C(=O)O)N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
AA0571:
id: AA0571
name: L-cysteine 5-methyloxazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-threonine
cyclase (EC 4.2.1.-); peptidyl-oxazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-[(1R)-1-azanyl-2-sulfanylethyl]-5-methyl-1,3-oxazole-4-carboxylic acid
- 2-[(1R)-1-amino-2-sulfanylethyl]-5-methyl-1,3-oxazole-4-carboxylic acid
identifiers:
- ns: mod
id: MOD:01900
- ns: resid
id: AA0571
structure: SC[C@@H](c1oc(c(n1)C(=O)O)C)N
base_monomers:
- T
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
AA0235:
id: AA0235
name: 4-hydroxy-L-lysine
comments: 5-Hydroxy-L-lysine (see RESID:AA0028) was found at a homologous position
in the closely related species Rhodomonas CS24. See also RESID:AA0370. The (2S,4R)
diastereomer is shown.
synonyms:
- alpha,epsilon-diamino-gamma-hydroxycaproic acid
- (2S,4R)-2,6-diamino-4-hydroxyhexanoic acid
- L-threo-gamma-hydroxylysine
identifiers:
- ns: go
id: GO:0018396
- ns: mod
id: MOD:00240
- ns: cas
id: 60594-62-9
- ns: resid
id: AA0235
structure: O[C@H](CC[NH3+])C[C@H]([NH3+])C(=O)O
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
- molecule: Monomer
element: H
position: 19
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
AA0457:
id: AA0457
name: L-cystine S-oxide
comments: This modification in the modeled protein has not been chemically confirmed.
synonyms:
- S-[(2R)-2-amino-3-oxopropyl] (2R)-2-amino-3-oxopropane-1-sulfinothioate
- cystine sulfoxide
- (2R)-2-amino-3-[([(2R)-2-amino-2-carboxyethyl]sulfanyl)sulfinyl]propanoic acid
- S-cysteinyl 3-(oxidosulfanyl)alanine
identifiers:
- ns: mod
id: MOD:01383
- ns: resid
id: AA0457
structure: O=C[C@H](CS[S@@](=O)C[C@@H](C(=O)O)[NH3+])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
C, G:
id: AA0188
name: L-cysteine 5-imidazolinone glycine
comments: This entry represents the cross-link of the peptide backbone from the
alpha-carboxyl carbon of residue N, a cysteine, to the alpha-amino nitrogen
of residue N+2, a glycine, coupled with the formation of a double bond to the
alpha-amino nitrogen of residue N+1 which loses one hydrogen, and the loss of
a molecule of water. This cross-link is accompanied by modification of residue
N+1. The modification of serine to dehydroalanine coupled with the formation
of 5-imidazolinone by the two neighboring residues produces the 4-methylidene-imidazole-5-one
(MIO) active site of some amino acid ammonia-lyases that differs by UV and mass
spectrometric evidence from other known dehydroalanine containing peptides not
containing the second modification.
synonyms:
- (2-[(1R)-1-amino-2-sulfanylethyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl)acetic
acid
- cysteinyl-5-imidazolinone glycine
- '[(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic
acid'
- '[(4z)-2-[(1r)-1-amino-2-mercaptoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic
acid'
- 2-[(4Z)-2-[(1R)-1-azanyl-2-sulfanyl-ethyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
- para-hydroxybenzylidene-imidazolidinone chromophore
- 2-[1-amino-2-sulfanylethyl]-1-carboxymethyl-1-imidazolin-5-one
- 4-methylidene-imidazole-5-one (MIO) active site
- CYG
identifiers:
- ns: resid
id: AA0188
- ns: mod
id: MOD:00196
- ns: pdb-ccd
id: GYC
- ns: go
id: GO:0018253
- ns: pdb.ligand
id: GYC
structure: OC(=O)CN1C(=NCC1=O)[C@@H]([NH3+])CS
base_monomers:
- C
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
AA0038:
id: AA0038
name: O-phospho-L-threonine
comments: 'Generating Enzyme: protein-threonine kinase (EC 2.7.1.37).'
synonyms:
- (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid
- 2-azanyl-3-(phosphonooxy)butanoic acid
- (2S,3R)-2-amino-3-phosphonooxy-butanoic acid
- T
- threonine phosphate ester
- 2-amino-3-hydroxybutanoic acid 3-phosphate
- O-phosphono-L-threonine
- O3-phosphothreonine
- phosphothreonine
identifiers:
- ns: resid
id: AA0038
- ns: go
id: GO:0018107
- ns: pdb-ccd
id: TPO
- ns: chebi
id: CHEBI:61971
- ns: mod
id: MOD:00047
- ns: pdb.ligand
id: TPO
- ns: cas
id: 1114-81-4
structure: OC(=O)[C@H]([C@H](OP(=O)([O-])[O-])C)[NH3+]
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
AA0542:
id: AA0542
name: 2'-hydroxy-L-tryptophan
comments: This modification may be produced artifactually.
synonyms:
- 2-azanyl-3-(2-hydroxy-1H-indol-3-yl)propanoic acid
- (2S)-2-amino-3-(2-hydroxy-1H-indol-3-yl)propanoic acid
- 2-hydroxy-tryptophan
- 2-hydroxy-L-tryptophan
identifiers:
- ns: pdb.ligand
id: TRO
- ns: resid
id: AA0542
- ns: mod
id: MOD:01816
structure: OC(=O)[C@H](Cc1c(O)[nH]c2c1cccc2)[NH3+]
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0447:
id: AA0447
name: (2S,3S,4R)-3,4-dihydroxyisoleucine
comments: In some cases the stereochemistry for the second and third chiral centers
have not been resolved.
synonyms:
- (2s,3s,4r)-2-amino-3,4-dihydroxy-3-methylpentanoic acid
- I
- beta,gamma-dihydroxyisoleucine
- (2S,3S,4R)-2-azanyl-3,4-dihydroxy-3-methyl-pentanoic acid
- (2S,3S,4R)-2-amino-3,4-dihydroxy-3-methylpentanoic acid (non-preferred name)
- (2S,3S,4R)-2-amino-3,4-dihydroxy-3-methylpentanoic acid
- (3S,4R)-3,4-dihydroxyisoleucine
identifiers:
- ns: pdb.ligand
id: TSI
- ns: resid
id: AA0447
- ns: pdb-ccd
id: TS9
- ns: mod
id: MOD:01376
structure: OC[C@H]([C@@]([C@H](O)C)(O)C)[NH3+]
base_monomers:
- I
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
AA0109:
id: AA0109
name: 2'-(S-L-cysteinyl)-L-histidine
comments: Cysteinylhistidine probably does not have a functional role in the enzymatic
activity of Neurospora crassa tyrosinase.
synonyms:
- (2S)-2-amino-3-[2-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-1H-imidazol-4-yl]propanoic
acid
- (2R)-2-amino-3-[(4-[(2S)-2-amino-2-carboxyethyl]-1H-imidazol-2-yl)sulfanyl]propanoic
acid
- S-(2'-histidyl)cysteine
identifiers:
- ns: mod
id: MOD:00118
- ns: go
id: GO:0018233
- ns: resid
id: AA0109
- ns: cas
id: 77504-36-0
structure: O=C[C@H](CSc1ncc([nH]1)C[C@@H](C(=O)O)[NH3+])[NH3+]
base_monomers:
- C
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
- molecule: Monomer
element: H
position: 18
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
AA0483:
id: AA0483
name: L-threonine thiazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-cysteine
cyclase (EC 4.2.1.-); peptidyl-thiazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-[1-azanyl-2-hydroxypropyl]-1,3-thiazole-4-carboxylic acid
- 2-[(1S,2R)-1-amino-2-hydroxypropyl]-1,3-thiazole-4-carboxylic acid
identifiers:
- ns: mod
id: MOD:01406
- ns: resid
id: AA0483
- ns: pdb.ligand
id: XAA
structure: C[C@H]([C@@H](c1scc(n1)C(=O)O)[NH3+])O
base_monomers:
- T
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
AA0237:
id: AA0237
name: O-(ADP-ribosyl)-L-serine
comments: 'It is not known whether botulinum exoenzyme C3 catalyzes formation
of the alpha or beta isomer. The alpha form is presented. The keyword "phosphoprotein"
is not used with toxin modification. Generating Enzyme: NAD(P)+--serine ADP-ribosyltransferase
(EC 2.4.2.-).'
synonyms:
- O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine
- (S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic
acid
- O3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen
diphosphate)
- O3-(ADP-ribosyl)-L-serine
identifiers:
- ns: go
id: GO:0006471
- ns: resid
id: AA0237
- ns: mod
id: MOD:00242
structure: OC(=O)[C@H](CO[C@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)(OP(=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)[O-])[O-])[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 51
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 51
- molecule: Monomer
element: H
position: 51
charge: 1
AA0346:
id: AA0346
name: N-glycyl-1-(phosphatidyl)ethanolamine
comments: A representative phospholipid structure is shown. Cleavage of a carboxyl
terminal propeptide accompanies transamidation.
synonyms:
- N-glycyl-1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
- (R)-1-hexadecanoyloxy-2-((Z)-9-octadecenoyloxy)-3-[2-(aminoacetylamino)ethyloxyphospho]propane
identifiers:
- ns: resid
id: AA0346
- ns: mod
id: MOD:00351
- ns: go
id: GO:0050495
structure: CCCCCCCCCCCCCCCC(=O)OC[C@@H](OC(=O)CCCCCCC/C=C\CCCCCCCC)CO[P@@](=O)(OCCNC(=O)C[NH3+])[O-]
base_monomers:
- G
l_bond_atoms:
- molecule: Monomer
element: N
position: 49
l_displaced_atoms:
- molecule: Monomer
element: H
position: 49
AA0064:
id: AA0064
name: N-methyl-L-methionine
comments: 'Polypeptides with monomethylated amino terminals can undergo premature
cleavage during the coupling step of an Edman degradation. This can result in
"preview" with both a residue and the following residue being seen from the
first step on through a sequence. Although appropriate, the keyword "thioether
bond" normally does not appear for this amino acid. Generating Enzyme: S-adenosylmethionine--methionyl-peptide
N-methyltransferase (EC 2.1.1.-).'
synonyms:
- (2S)-2-methylamino-4-(methylsulfanyl)butanoic acid
- n-methyl methionine
- M
- N-methyl-L-methionine
- 2-methylamino-4-(methylthio)butanoic acid
- (2S)-2-methylamino-4-methylsulfanyl-butanoic acid
- N-methylmethionine
identifiers:
- ns: go
id: GO:0018014
- ns: cas
id: 42537-72-4
- ns: pdb-ccd
id: MME
- ns: pdb.ligand
id: MME
- ns: resid
id: AA0064
- ns: chebi
id: CHEBI:61886
- ns: mod
id: MOD:00073
structure: CSCC[C@@H](C(=O)O)[NH2+]C
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
AA0385:
id: AA0385
name: O-decanoyl-L-serine
comments: 'Generating Enzyme: ghrelin O-acyltransferase, GOAT (EC 2.3.1.-).'
synonyms:
- L-serine decanoate ester
- (2S)-2-amino-3-(decanoyloxy)propanoic acid
- O3-decanoyl-L-serine
identifiers:
- ns: mod
id: MOD:00390
- ns: resid
id: AA0385
- ns: go
id: GO:0042050
structure: CCCCCCCCCC(=O)OC[C@@H](C(=O)O)[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
- molecule: Monomer
element: H
position: 18
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
AA0390:
id: AA0390
name: O4-(N-acetylamino)glucosyl-L-hydroxyproline
comments: See also RESID:AA0212 and RESID:AA0389 for other O4-glycosylated 4-hydroxyprolines.
synonyms:
- 4-(N-acetylglucosaminyloxy)proline
- (2S,4R)-4-[2-acetamido-2-deoxy-alpha-D-glucopyranosyloxy]pyrrolidine-2-carboxylic
acid
- 4-[(2-N-acetylamino)-alpha-D-glucopyranosyl]oxyproline
- O4-glycosyl-hydroxyproline
- alpha-2-(N-acetylamino)glucopyranosyl-4-hydroxyproline
identifiers:
- ns: resid
id: AA0390
- ns: cas
id: 10036-64-3
- ns: mod
id: MOD:00758
structure: OC[C@H]1O[C@H](O[C@H]2C[NH2+][C@@H](C2)C(=O)O)[C@@H]([C@H]([C@@H]1O)O)NC(=O)C
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
- molecule: Monomer
element: H
position: 20
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
E, Y:
id: AA0283
name: pyrroloquinoline quinone
comments: In some prokaryotes, the pqqA protein is the origin of pyrroloquinoline
quinone. In other organisms the endogenous source, if there is one, has not
been established.
synonyms:
- 4,5-dihydro-4,5-dioxo-1H-pyrrolo[2,3-5,6]quinoline-2,7,9-tricarboxylic acid
- 2,7,9-tricarboxy-1H-pyrrolo(2,3-f)quinoline-4,5-dione
- coenzyme PQQ
- methoxatin
- 2,4,6-tricarboxylic-pyrrolo[2,3-5,6]quinoline 8,9-quinone
identifiers:
- ns: resid
id: AA0283
- ns: pdb.ligand
id: PQQ
- ns: cas
id: 72909-34-3
- ns: chebi
id: CHEBI:18315
- ns: go
id: GO:0018189
- ns: mod
id: MOD:00288
structure: '[O-]C(=O)c1cc(nc2c1c1[nH]c(cc1C(=O)C2=O)C(=O)[O-])C(=O)[O-]'
base_monomers:
- E
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 23
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
AA0402:
id: AA0402
name: O-mannosyl-L-serine
comments: 'See also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291,
RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0404,
RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines. Generating
Enzyme: dolichyl-phosphate-mannose-protein mannosyltransferase (EC 2.4.1.109).'
synonyms:
- O-mannopyranosylserine
- O3-mannosylserine
- (2S)-2-amino-3-(alpha-D-mannopyranosyloxy)propanoic acid
- O-glycosylserine
identifiers:
- ns: resid
id: AA0402
- ns: mod
id: MOD:00810
- ns: cas
id: 78609-14-0
structure: OC[C@H]1O[C@H](OC[C@@H](C(=O)O)[NH3+])[C@H]([C@H]([C@@H]1O)O)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0145:
id: AA0145
name: O4'-(8alpha-FAD)-L-tyrosine
comments: 'The keyword "phosphoprotein" is not used with flavin modifications
linked through the flavin. Generating Enzyme: autocatalytic.'
synonyms:
- (2S)-2-amino-3-(4-[8alpha-riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester
with adenosine]oxyphenyl)propanoic acid
- 8alpha-(O4'-tyrosyl)FAD
identifiers:
- ns: go
id: GO:0018296
- ns: pdb.ligand
id: FAD
- ns: resid
id: AA0145
- ns: mod
id: MOD:00154
structure: O=C1[N-]C(=O)C2C(N1)N(C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O[P@@](=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc3c1ncnc3N)[O-])[O-])O)O)O)C1C(N2)CC(C(C1)COc1ccc(cc1)C[C@@H](C(=O)O)[NH3+])C
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 70
l_bond_atoms:
- molecule: Monomer
element: N
position: 73
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 72
- molecule: Monomer
element: H
position: 72
l_displaced_atoms:
- molecule: Monomer
element: H
position: 73
- molecule: Monomer
element: H
position: 73
charge: 1
AA0476:
id: AA0476
name: N6-(ADP-ribosyl)-L-lysine
comments: 'The alpha form is presented. The keyword "phosphoprotein" is not used
with ADP-ribosylation. Generating Enzyme: NAD(P)+--lysine ADP-ribosyltransferase
(EC 2.4.2.-).'
synonyms:
- N6-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-lysine
- 2-amino-6-(ADP-ribosyl)amino-hexanoic acid
- epsilon-ADP-ribosyllysine
- (S)-2-amino-6-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)hexanoic
acid
- N(zeta)-ADP-ribosyllysine
- N6-alpha-D-ribofuranosyl-L-lysine 5'->5'-ester with adenosine 5'-(trihydrogen
diphosphate)
identifiers:
- ns: mod
id: MOD:01399
- ns: resid
id: AA0476
structure: OC(=O)[C@H](CCCC[NH2+][C@H]1O[C@@H]([C@H]([C@H]1O)O)CO[P@](=O)(O[P@@](=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1NC=N[C@H]2N)[O-])[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 57
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 57
- molecule: Monomer
element: H
position: 57
charge: 1
AA0153:
id: AA0153
name: O5-glucosylgalactosyl-L-hydroxylysine
comments: 'Some forms of lysyl hydroxylase (EC 1.14.11.4) are multifunctional
and possess both transferase activities. Generating Enzyme: procollagen galactosyltransferase
(EC 2.4.1.50); procollagen glucosyltransferase (EC 2.4.1.66).'
synonyms:
- (2S,5R)-2,6-diamino-5-[2-O-(alpha-D-glucopyranosyl)-beta-D-galactopyranosyloxy]hexanoic
acid
- 5-(2-O-alpha-D-glucopyranosyl-beta-D-galactopyranosyl)oxy-L-lysine
identifiers:
- ns: go
id: GO:0006493
- ns: resid
id: AA0153
- ns: cas
id: 32448-35-4
- ns: mod
id: MOD:00162
structure: OC[C@H]1O[C@@H](O[C@H](CC[C@@H](C(=O)O)[NH3+])C[NH3+])[C@@H]([C@H]([C@H]1O)O)O[C@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
- molecule: Monomer
element: H
position: 17
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0594:
id: AA0594
name: labionine
comments: This three residue cross-link modification includes both a thioether
bond and an alpha-linked carbon-carbon bond.
synonyms:
- (2S,4S)-2,4-diamino-2-[([(2R)-2-amino-2-carboxyethyl]sulfanyl)methyl]pentanedioic
acid
- (2S,4S,8R)-labionin
- (2S,4S,8R)-2,4,8-triamino-4-carboxy-6-thianonanedioic acid
identifiers:
- ns: mod
id: MOD:01948
- ns: resid
id: AA0594
structure: O=C[C@H](CSC[C@](C[C@@H](C(=O)O)[NH3+])(C=O)N)[NH3+]
base_monomers:
- S
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0434:
id: AA0434
name: hydroxyglycine
comments: The S form, produced by peptidylglycine alpha-hydroxylating monooxygenase,
is shown.
synonyms:
- aminohydroxyacetic acid
- amino(hydroxy)acetic acid
- alpha-hydroxyglycine
identifiers:
- ns: chebi
id: CHEBI:38048
- ns: mod
id: MOD:01180
- ns: resid
id: AA0434
- ns: cas
id: 4746-62-7
structure: OC(=O)[C@H](O)N
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
AA0531:
id: AA0531
name: 5-hydroxy-N6-(beta-lysyl)-L-lysine
comments: 'This modification is produced from N6-acylation of lysine by a lysyl-adenylate.
However, evidence on whether alpha- or beta-lysyl adenylate is used, and the
intermediates on the pathway appears to be in conflict (see RESID:AA0530). The
modified lysine residue is homologous to the lysine modified to hypusine in
eukaryotic and archaeal translation initiation factor 5A. The structure of this
modification has not been established. The original proposed structure was not
hydroxylated. Neither the location of the hydroxyl, shown as a 5-hydroxy, or
its stereochemistry is known. Generating Enzyme: translation elongation factor
P-lysine 2,3-aminomutase YjeK (EC 5.4.3.-); translation elongation factor P-lysine
monooxygenase YfcM (EC 1.14.99.-).'
synonyms:
- lysyl spermidine derivative [misidentification]
- (2S)-2-amino-6-([(3R)-3,6-diaminohexanoyl]amino)-5-hydroxyhexanoic acid
- EF-P lysine derivative
- N6-[(3R)-3,6-diaminohexanoyl]-L-5-hydroxylysine
- 5-hydroxy-N6-[(3R)-beta-lysyl]lysine
identifiers:
- ns: mod
id: MOD:01780
- ns: go
id: GO:0072580
- ns: resid
id: AA0531
structure: '[NH3+]CCC[C@@H](CC(=O)NC[C@@H](CC[C@@H](C(=O)O)[NH3+])O)[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 21
l_bond_atoms:
- molecule: Monomer
element: N
position: 24
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 23
- molecule: Monomer
element: H
position: 23
l_displaced_atoms:
- molecule: Monomer
element: H
position: 24
- molecule: Monomer
element: H
position: 24
charge: 1
AA0320:
id: AA0320
name: L-beta-methylthioasparagine
comments: There is a second chiral center. The (2R,3R) form is shown. This modification
was predicted for ribosomal protein S12 in Bacillus subtilis when the sequence
in the original version of the genome was reported to have asparagine rather
than aspartic acid at the position of the methylthioaspartic acid modification
(see RESID:AA0232). Two groups independently confirmed that the genome sequence
was erroroneous. The sequence in the revised genome has aspartic acid at that
position.
synonyms:
- 3-carboxamido-S-methyl-cysteine
- beta-(methylthio)asparagine
- (2R,3Xi)-2-amino-3-(methylsulfanyl)-4-butanediamic acid
- 2,4-diamino-3-(methylsulfanyl)-4-oxobutanoic acid
identifiers:
- ns: resid
id: AA0320
- ns: mod
id: MOD:00325
- ns: go
id: GO:0042259
structure: CS[C@H]([C@@H](C(=O)O)N)C(=O)N
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
H, Y:
id: AA0270
name: 3'-(1'-L-histidyl)-L-tyrosine
comments: This modification is different from the modification 3-(3'-L-histidyl)-L-tyrosine,
see RESID:AA0250.
synonyms:
- (2S)-2-amino-3-[1-(5-[(2S)-2-amino-2-carboxyethyl]-2-hydroxyphenyl)-1H-imidazol-4-yl]propanoic
acid
- 3'-(tele-histidyl)tyrosine
- 3'-(tau-histidyl)tyrosine
- 3'-(N(epsilon)-histidyl)tyrosine
- 3'-(N1'-histidyl)tyrosine
identifiers:
- ns: chebi
id: CHEBI:19837
- ns: mod
id: MOD:00275
- ns: go
id: GO:0018152
- ns: resid
id: AA0270
structure: O=C[C@H](Cc1ccc(c(c1)n1cnc(c1)C[C@@H](C(=O)O)[NH3+])O)[NH3+]
base_monomers:
- Y
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 23
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: H
position: 23
- molecule: Monomer
element: H
position: 23
charge: 1
AA0471:
id: AA0471
name: cysteine-5-amino-3,4,5,6-tetrahydropyridine-2,5-dicarboxylic acid
comments: Formed by the metathesis of two didehydroalanines made from serines,
condensation with a cysteine carbonyl and dehydrogenation.
synonyms:
- (5R,6R)-5-amino-6-[(1R)-1-amino-2-sulfanylethyl]-3,4,5,6-tetrahydropyridine-2,5-dicarboxylic
acid
- L-cysteine 5-aminopiperideine-2,5-dicarboxylic acid
identifiers:
- ns: resid
id: AA0471
- ns: mod
id: MOD:01394
- ns: pdb.ligand
id: XBB
structure: SC[C@@H]([C@H]1N=C(CC[C@]1(N)C=O)C(=O)O)[NH3+]
base_monomers:
- S
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
- molecule: Monomer
element: H
position: 17
AA0116:
id: AA0116
name: N6-(4-amino-2-hydroxybutyl)-L-lysine
comments: 'Hypusine appears to occur uniquely in translation initiation factor
eIF-5A. For the detectable intermediate form, L-deoxyhypusine, in either deoxyhypusine
synthase or in initiation factor 5A, eIF5A, see RESID:AA0564. It is highly probable
that, like prokaryotic elongation factor EF-P, eIF-5A acts to relieve ribosome
stalling during the translation of polyproline and prolylglycine sequences.
The hypusine residue may extend into the ribosome active site and assist in
catalysis of the petidyl transfer. Generating Enzyme: deoxyhypusine synthase
(EC 2.5.1.46); deoxyhypusine monooxygenase (EC 1.14.99.29).'
synonyms:
- N6-(4-amino-2-hydroxybutyl)-L-lysine
- (2S)-2-amino-6-([(2R)-4-amino-2-hydroxybutyl]amino)hexanoic acid
- (2S,9R)-2,11-diazanyl-9-hydroxy-7-azaundecanoic acid
- (2S,9R)-hypusine
- 2-azanyl-6-[(4-azanyl-2-hydroxybutyl)azanyl]hexanoic acid
identifiers:
- ns: mod
id: MOD:00125
- ns: go
id: GO:0008612
- ns: chebi
id: CHEBI:21858
- ns: resid
id: AA0116
- ns: cas
id: 34994-11-1
structure: '[NH3+]CC[C@H](C[NH2+]CCCC[C@@H](C(=O)O)[NH3+])O'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 19
l_bond_atoms:
- molecule: Monomer
element: N
position: 22
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 21
- molecule: Monomer
element: H
position: 21
l_displaced_atoms:
- molecule: Monomer
element: H
position: 22
- molecule: Monomer
element: H
position: 22
charge: 1
AA0568:
id: AA0568
name: N6-malonyl-L-lysine
comments: The responsible generating enzyme activity is not identified. This modification
can be reversed by Sirt5.
synonyms:
- N6-(carboxyacetyl)lysine
- N6-malonyllysine
- N(epsilon)-(malonyl)lysine
- malonyllysine
- 2-azanyl-6-[(carboxyacetyl)azanyl]hexanoic acid
- (2S)-2-amino-6-[(carboxyacetyl)amino]hexanoic acid
identifiers:
- ns: go
id: GO:0044392
- ns: mod
id: MOD:01893
- ns: resid
id: AA0568
structure: O=C[C@H](CCCCNC(=O)CC(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
AA0223:
id: AA0223
name: S-diphytanylglycerol diether-L-cysteine
comments: The stereochemistry of the glycerol has not been determined. The S form
is shown.
synonyms:
- (2R)-2-amino-3-([(2S)-2,3-bis(3,7,11,15-tetramethylhexadecanyloxy)propyl]sulfanyl)propanoic
acid
- S-[2',3'-bis(phytanyloxy)propyl]cysteine
- S-archaeol cysteine
identifiers:
- ns: resid
id: AA0223
- ns: mod
id: MOD:00228
- ns: go
id: GO:0018115
structure: C[C@H](CCC[C@@H](CCC[C@@H](CCCC(C)C)C)C)CCOC[C@@H](CSC[C@@H](C(=O)O)[NH3+])OCC[C@@H](CCC[C@@H](CCC[C@@H](CCCC(C)C)C)C)C
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 33
l_bond_atoms:
- molecule: Monomer
element: N
position: 36
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 35
- molecule: Monomer
element: H
position: 35
l_displaced_atoms:
- molecule: Monomer
element: H
position: 36
- molecule: Monomer
element: H
position: 36
charge: 1
AA0407:
id: AA0407
name: S-stearoyl-L-cysteine
comments: 'Although the predominant palmitoyl transferase in mammalian systems
appears to utilize a mixture of saturated and unsaturated fatty acids, some
systems may be more specific in their incorporation of other fatty acids. See
RESID:AA0307 and RESID:AA0308. This modification may be misidentified as S-palmitoyl-cysteine
(see RESID:AA0106) when labeled palmitate is used without determining whether
metabolic conversion has occurred. Generating Enzyme: protein-cysteine S-stearoyltransferase
(EC 2.3.1.-).'
synonyms:
- (R)-2-amino-3-(octadecanoylsulfanyl)propanoic acid
- 2-amino-3-(octadecanoylthio)propanoic acid
- cysteine octadecanoate thioester
- cysteine stearate thioester
identifiers:
- ns: mod
id: MOD:00816
- ns: resid
id: AA0407
structure: CCCCCCCCCCCCCCCCCC(=O)SC[C@@H](C(=O)O)N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 24
l_bond_atoms:
- molecule: Monomer
element: N
position: 27
r_displaced_atoms:
- molecule: Monomer
element: O
position: 26
- molecule: Monomer
element: H
position: 26
l_displaced_atoms:
- molecule: Monomer
element: H
position: 27
AA0509:
id: AA0509
name: 3'-iodo-L-tyrosine
synonyms:
- (2S)-2-amino-3-(4-hydroxy-3-iodophenyl)propanoic acid
- 4-hydroxy-3-iodo-phenylalanine
- MIT
- 3-iodo-tyrosine
- 3-iodo-L-tyrosine
- (2S)-2-amino-3-(4-hydroxy-3-iodo-phenyl)propanoic acid
- Y
- 3-iodotyrosine
identifiers:
- ns: chebi
id: CHEBI:27847
- ns: pdb.ligand
id: IYR
- ns: resid
id: AA0509
- ns: cas
id: 70-78-0
- ns: mod
id: MOD:01612
- ns: pdb-ccd
id: IYR
structure: OC(=O)[C@H](Cc1ccc(c(c1)I)O)[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0445:
id: AA0445
name: (2S,4R)-4,5-dihydroxyleucine
synonyms:
- gamma,delta-dihydroxyleucine
- (2S,4R)-2-amino-4,5-dihydroxy-4-methylpentanoic acid (non-preferred name)
- (2s,4r)-2-amino-4,5-dihydroxy-4-methylpentanoic acid
- (2S,4R)-2-amino-4,5-dihydroxy-4-methylpentanoic acid
- (2~{S},4~{R})-2-azanyl-4-methyl-4,5-bis(oxidanyl)pentanoic acid
- (4R)-4,5-dihydroxyleucine
identifiers:
- ns: mod
id: MOD:01375
- ns: resid
id: AA0445
- ns: pdb-ccd
id: EEP
structure: OC[C@@](C[C@@H](C(=O)O)[NH3+])(O)C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
U:
id: AA0022
name: L-selenocysteine
comments: 'Selenocysteine is translated for the UGA codon in some genetic systems.
It has not yet been demonstrated to arise alternatively from a post-translational
modification. Although the single letter symbol U is recommended by IUBMB, many
software applications fail to recognize it, and some sequence databases may
use the single letter symbol C. Generating Enzyme: serine--tRNA ligase (EC 6.1.1.11);
L-seryl-tRNA(Sec) selenium transferase, SelA (EC 2.9.1.1); O-phosphoseryl-tRNA(Sec)
kinase (EC 2.7.1.164); O-phospho-L-seryl-tRNA(Sec):L-selenocysteinyl-tRNA synthase,
SepSecS (EC 2.9.1.2).'
synonyms:
- selenium cysteine
- 2-azanyl-3-selanylpropanoic acid
- 3-selenylalanine
- (2R)-2-amino-3-selanylpropanoic acid
- SeCys
identifiers:
- ns: mod
id: MOD:00031
- ns: chebi
id: CHEBI:30000
- ns: cas
id: 10236-58-5
- ns: resid
id: AA0022
- ns: go
id: GO:0001514
- ns: pdb.ligand
id: CSE
- ns: mod
id: MOD:00686
structure: N[C@H](C(=O)O)C[SeH]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0229:
id: AA0229
name: L-cysteine glutathione disulfide
comments: Disulfide formation with free glutatione extracellularly is probably
not enzymatically catalyzed.
synonyms:
- cysteinyl glutathione
- L-gamma-glutamyl-L-cysteinyl-glycine (2-1')-disulfide with L-cysteine
- N-(N-gamma-glutamyl-cystinyl)-glycine
- (2S)-2-amino-3-((2S)-2-((4R)-4-amino-4-carboxyl-1-oxobutyl)amino-3-(carboxylmethyl)amino-3-oxo-propyl)dithio-propanoic
acid
identifiers:
- ns: chebi
id: CHEBI:21264
- ns: go
id: GO:0018118
- ns: resid
id: AA0229
- ns: cas
id: 13081-14-6
- ns: mod
id: MOD:00234
- ns: pdb.ligand
id: GSH
structure: O=C[C@H](CSSC[C@@H](C(=O)NCC(=O)[O-])NC(=O)CC[C@@H](C(=O)[O-])[NH3+])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
AA0426:
id: AA0426
name: S-(15-deoxy-Delta12,14-prostaglandin J2-9-yl)-L-cysteine
comments: 'Generating Enzyme: autocatalytic.'
synonyms:
- (5Z,9Xi,12E,14Z)-9-([(2R)-2-amino-3-carboxyethyl]sulfanyl)-11-oxoprosta-5,12,14-trien-1-oic
acid
- (2R)-2-amino-3-([(5Z,9Xi,12E,14Z)-1-hydroxy-1,11-oxoprosta-5,12,14-trien-9-yl]sulfanyl)propanoic
acid
identifiers:
- ns: cas
id: 60203-57-8
- ns: chebi
id: CHEBI:27485
- ns: mod
id: MOD:01174
- ns: resid
id: AA0426
structure: CCCCC/C=C\C=C/1\C(=O)C[C@H]([C@@H]1C/C=C\CCCC(=O)[O-])SC[C@@H](C=O)[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 23
l_bond_atoms:
- molecule: Monomer
element: N
position: 32
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 32
- molecule: Monomer
element: H
position: 32
charge: 1
AA0458:
id: AA0458
name: aminomalonic acid
comments: This modification in the modeled protein has not been chemically confirmed.
As a free amino acid, aminomalonic acid is achiral. However, originating from
(2S)-serine in a protein, the residue would be named as a (2R)-2,3-diamino-3-oxopropanoic
acid, with the serine carbon-3 carboxyl taking precedence, becoming carbon-1,
and changing the stereochemical designation. The PDB Hetgroup FGL was originally
designated as the "C(alpha)-formyl glycine" active site residue L-3-oxoalanine
(see RESID:AA0185) observed in its hydrated form. That structure, a gem-diol
with an sp(3) carbon, was misinterpreted as a carboxyl with an sp(2) carbon
and assigned to aminomalonic acid instead.
synonyms:
- 2-carboxyglycine
- aminopropanedioic acid
- Ama
identifiers:
- ns: mod
id: MOD:01384
- ns: resid
id: AA0458
- ns: pdb.ligand
id: FGL
- ns: cas
id: 1068-84-4
structure: O=C[C@H](C(=O)[O-])[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
AA0590:
id: AA0590
name: N6-oleoyl-L-lysine
comments: 'Generating Enzyme: peptidyl-lysine N6-oleoyltransferase (EC 2.3.1.-).'
synonyms:
- N6-[(9Z)-1-oxo-9-octadecenyl]lysine
- (2S)-2-amino-6-([(9Z)-octadec-9-enoyl]amino)hexanoic acid
identifiers:
- ns: cas
id: 23499-75-4
- ns: resid
id: AA0590
- ns: mod
id: MOD:01936
structure: CCCCCCCC/C=C\CCCCCCCC(=O)NCCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 27
l_bond_atoms:
- molecule: Monomer
element: N
position: 30
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 29
- molecule: Monomer
element: H
position: 29
l_displaced_atoms:
- molecule: Monomer
element: H
position: 30
- molecule: Monomer
element: H
position: 30
charge: 1
AA0305:
id: AA0305
name: N5-methyl-L-arginine
comments: 'This modification should not be confused with 5-methylarginine (see
RESID:AA0272). Generating Enzyme: protein-arginine N5-methyltransferase (EC
2.1.1.-).'
synonyms:
- (2S)-2-amino-5-(N-methylcarbamimidamido)pentanoic acid
- N5-carbamimidoyl-N5-methyl-L-ornithine
- delta-N-methylarginine
identifiers:
- ns: mod
id: MOD:00310
- ns: go
id: GO:0019701
- ns: resid
id: AA0305
- ns: chebi
id: CHEBI:21848
structure: OC(=O)[C@H](CCCN(C(=[NH2])N)C)[NH3+]
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0541:
id: AA0541
name: L-glutamate thiazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. This modification is currently
represented in the PDB as part of the HET group for the entire molecule of nosiheptide.
Generating Enzyme: peptidyl-cysteine cyclase (EC 4.2.1.-); peptidyl-thiazoline
dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-[-1-azanyl-3-carboxypropyl]-1,3-thiazole-4-carboxylic acid
- 2-[(1S)-1-amino-3-carboxypropyl]-1,3-thiazole-4-carboxylic acid
identifiers:
- ns: mod
id: MOD:01815
- ns: pdb.ligand
id: BB9
- ns: resid
id: AA0541
structure: O=Cc1csc(n1)[C@@H](CCC(=O)[O-])[NH3+]
base_monomers:
- E
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
AA0325:
id: AA0325
name: (phospho-5'-guanosine)-L-histidine
comments: It is not known whether the phosphoramide bond is formed with the tele-
or pros-nitrogen of histidine. The tele-linked form is presented.
synonyms:
- tele-5'-guanylic-L-histidine
- L-histidine 5'-guanosine phosphoramidester
- L-histidine monoanhydride with 5'-guanylic acid
- (2S)-2-amino-3-(1-(5'-adenosine phosphono)imidazol-4-yl)propanoic acid
- N1'-guanylylated histidine
- N(tau)-5'-guanylic-L-histidine
identifiers:
- ns: go
id: GO:0045427
- ns: mod
id: MOD:00330
- ns: pdb.ligand
id: 5GP
- ns: resid
id: AA0325
structure: OC(=O)[C@H](Cc1ncn(c1)[P@@](=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1nc(N)[nH]c2=O)[O-])[NH3+]
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 40
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 40
- molecule: Monomer
element: H
position: 40
charge: 1
AA0082:
id: AA0082
name: L-arginine amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- amino{[(4S)-4,5-diamino-5-oxopentyl]amino}methaniminium
- '[amino-[[(4S)-4,5-diamino-5-oxo-pentyl]amino]methylidene]azanium'
- arginineamide
- (2S)-2-amino-5-[(diaminomethylidene)amino]pentanamide
- argininamide
- R
- 2-amino-5-carbamimidamidopentanamide
- 2-amino-5-guanidinopentanamide
identifiers:
- ns: cas
id: 2788-83-2
- ns: go
id: GO:0018035
- ns: pdb-ccd
id: AAR
- ns: resid
id: AA0082
- ns: mod
id: MOD:00091
- ns: pdb.ligand
id: AAR
- ns: chebi
id: CHEBI:21236
structure: NC(=[NH+]CCC[C@@H](C(=O)N)[NH3+])N
base_monomers:
- R
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0480:
id: AA0480
name: (2S)-4,5,5'-trihydroxyleucine
synonyms:
- (2S)-2-amino-4,5-dihydroxy-4-(hydroxymethyl)pentanoic acid
- 4,5,5'-trihydroxyleucine
- gamma,delta,delta'-trihydroxyleucine
identifiers:
- ns: resid
id: AA0480
- ns: mod
id: MOD:01403
structure: OCC(C[C@@H](C(=O)O)N)(CO)O
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
AA0044:
id: AA0044
name: N-acetyl-L-glutamic acid
comments: 'Generating Enzyme: peptide alpha-N-acetyltransferase (EC 2.3.1.88).'
synonyms:
- 2-(acetylamino)pentanedioic acid
- 2-(acetylazanyl)pentanedioic acid
- acetylglutamic acid
- (2S)-2-(acetamido)pentanedioic acid
identifiers:
- ns: cas
id: 1188-37-0
- ns: go
id: GO:0018002
- ns: resid
id: AA0044
- ns: chebi
id: CHEBI:17533
- ns: mod
id: MOD:00053
structure: O=C[C@@H](NC(=O)C)CCC(=O)[O-]
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
AA0299:
id: AA0299
name: L-leucine methyl ester
comments: 'The carboxy-terminal motif for this modification, [PAMV][DG]YFL*, is
strongly conserved. Generating Enzyme: [phosphatase 2A protein]-leucine-carboxy
methyltransferase (EC 2.1.1.233).'
synonyms:
- 2-amino-4-methylpentanoic methyl ester
- methyl (2S)-2-amino-4-methylpentanoate
- methyl l-leucinate
- alpha-aminoisocaproic methyl ester
- methyl (2S)-2-amino-4-methyl-pentanoate
- methyl L-leucinate
- L
identifiers:
- ns: mod
id: MOD:00304
- ns: chebi
id: CHEBI:44075
- ns: pdb-ccd
id: MLL
- ns: go
id: GO:0018439
- ns: resid
id: AA0299
- ns: cas
id: 2666-93-5
- ns: pdb.ligand
id: MLL
structure: COC(=O)[C@H](CC(C)C)[NH3+]
base_monomers:
- L
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
AA0115:
id: AA0115
name: N6-1-carboxyethyl-L-lysine
comments: 'Generating Enzyme: autocatalytic.'
synonyms:
- NZ-(1-carboxyethyl)lysine
- (2S)-2-amino-6-([(1S)-1-carboxyethyl]amino)hexanoic acid
- N6-(1-carboxyethyl)lysine
identifiers:
- ns: mod
id: MOD:00124
- ns: cas
id: 68852-50-6
- ns: chebi
id: CHEBI:53015
- ns: go
id: GO:0018238
- ns: resid
id: AA0115
- ns: pdb.ligand
id: MCL
structure: O=C[C@H](CCCC[NH2+][C@H](C(=O)[O-])C)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
AA0080:
id: AA0080
name: O-palmitoyl-L-serine
comments: The palmitate represents a mixture of saturated and unsaturated fatty
acids.
synonyms:
- (2S)-2-amino-3-(hexadecanoyloxy)propanoic acid
- serine palmitate ester
- O3-palmitoyl-serine
- L-serine hexadecanoate ester
identifiers:
- ns: pdb.ligand
id: PLM
- ns: cas
id: 88815-78-5
- ns: go
id: GO:0018221
- ns: mod
id: MOD:00089
- ns: resid
id: AA0080
structure: CCCCCCCCCCCCCCCC(=O)OC[C@@H](C(=O)O)[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 22
l_bond_atoms:
- molecule: Monomer
element: N
position: 25
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 24
- molecule: Monomer
element: H
position: 24
l_displaced_atoms:
- molecule: Monomer
element: H
position: 25
- molecule: Monomer
element: H
position: 25
charge: 1
AA0610:
id: AA0610
name: 3-methyl-L-lanthionine
comments: "There are 3 chiral centers, so there are 8 possible stereoisomers.\
\ Bacterial peptidyl-cysteine dehydroalanine/dehydrobutyrine ligase and peptide\
\ conformation preferentially produce the (2S,3S,2'R) diastereomer. The cysteine\
\ maintains its L configuration (R chirality), while the threonine 2-aminobutanoate\
\ skeleton koses and then regains an L configuration (R chirality). For the\
\ (2S,3S,2'R), see RESID:AA0112. Generating Enzyme: peptidyl-phosphoserine/phosphothreonine\
\ dehydratase (EC 4.2.1.-); peptidyl-cysteine dehydroalanine/dehydrobutyrine\
\ ligase (EC 6.2.-.-)."
synonyms:
- cysteine-3-L-butyrine thioether
- 3-methyl-L,L-lanthionine
- 2-azanyl-3-[(2-azanyl-2-carboxyethyl)sulfanyl]butanoic acid
- (2R,3R,2'R)-2-amino-3-[(2-amino-2-carboxyethyl)thio]butanoic acid
- (2R,3R,6R)-3-methyllanthionine
- (2R,3R)-2-amino-3-([(2R)-2-amino-2-carboxyethyl]sulfanyl)butanoic acid
- (2R,3R,6R)-2,6-diamino-3-methyl-4-thiaheptanedioic acid
identifiers:
- ns: mod
id: MOD:01968
- ns: resid
id: AA0610
structure: O=C[C@H](CS[C@@H]([C@@H](C(=O)O)[NH3+])C)[NH3+]
base_monomers:
- T
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
AA0420:
id: AA0420
name: N4-(N-acetylamino)galactosyl-L-asparagine
comments: This modification occurs in archaebacterial cell surface proteins with
an NX[ST] motif. See also RESID:AA0151 and RESID:AA0421 for other N4-glycosylated
asparagines.
synonyms:
- N4-(2-acetamido-2-deoxy-beta-D-galactopyranosyl)-L-asparagine
- N4-asparagine-beta-N-acetylgalactosaminide
- N4-glycosylasparagine
- N4-glycosyl-L-asparagine
- (2S)-2-amino-4-(2-acetamido-2-deoxy-beta-D-galactopyranosyl)amino-4-oxobutanoic
acid
- N4-(N-acetylgalactosaminyl)asparagine
- N4-(2-acetylamino-2-deoxy-beta-D-galactopyranosyl)-L-asparagine
identifiers:
- ns: resid
id: AA0420
- ns: mod
id: MOD:00832
- ns: cas
id: 100991-94-4
structure: OC[C@H]1O[C@H](NC(=O)C[C@@H](C(=O)O)N)[C@@H]([C@H]([C@H]1O)O)NC(=O)C
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
- molecule: Monomer
element: H
position: 16
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
AA0607:
id: AA0607
name: N4-(2,4-diacetamido-2,4,6-trideoxy-D-glucosyl)-L-serine
comments: Bacillosamine is a trivial name formed by modification of a non-standard
monosaccharide parent name, and is not recommended by the IUPAC Nomenclature
Committee. Some authors use bacillosamine to refer to the diacetylated form,
rather than the unacetylated form. For O-(2,4-diacetamido-2,4-dideoxy-D-glucosyl)-L-serine,
see RESID:AA0499.
synonyms:
- DATDH
- O-[N2,N4-diacetylbacillosaminyl]serine
- DABA
- (2S)-2-amino-4-[(2,4-diacetamido-2,4,6-trideoxy-beta-D-glucopyranosyl)oxy]propanoic
acid
- DiNAcBac
- O-[N,N-diacetylbacillosaminyl]serine
- O-[2,4-bis(acetylamino)-2,4,6-trideoxy-beta-D-glucopyranosyl]-L-serine
identifiers:
- ns: resid
id: AA0607
- ns: mod
id: MOD:01963
structure: CC(=O)N[C@H]1[C@H](OC[C@@H](C(=O)O)[NH3+])O[C@@H]([C@H]([C@@H]1O)NC(=O)C)C
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0047:
id: AA0047
name: N-acetyl-L-isoleucine
comments: The occurrence of this modification has not been confirmed.
synonyms:
- 2-acetylamino-3-methylpentanoic acid
- 2-acetylazanyl-3-methylpentanoic acid
- acetylisoleucine
- (2S,3S)-2-acetamido-3-methylpentanoic acid
identifiers:
- ns: resid
id: AA0047
- ns: mod
id: MOD:00056
- ns: chebi
id: CHEBI:21555
- ns: cas
id: 3077-46-1
- ns: go
id: GO:0017194
structure: CC[C@@H]([C@@H](C(=O)O)NC(=O)C)C
base_monomers:
- I
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
AA0219:
id: AA0219
name: 1-chondroitin sulfate-L-aspartic acid ester
synonyms:
- poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate D-galactosyl)]beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate-6-(1-L-aspartyl)-D-galactose)
- protein-glycosaminoglycan-protein cross-link
- 1-aspartic acid ester with 6-chondroitin 4-sulfate
identifiers:
- ns: mod
id: MOD:00224
- ns: resid
id: AA0219
- ns: go
id: GO:0019800
structure: CC(=O)N[C@H]1[C@H](O)O[C@@H]([C@@H]([C@@H]1O[C@@H]1O[C@@H](C[C@@H]([C@H]1O)O)C(=O)[O-])OS(=O)(=O)[O-])COC(=O)[C@H](CC(=O)[O-])[NH3+]
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 30
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 32
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
AA0217:
id: AA0217
name: 2'-alpha-mannosyl-L-tryptophan
comments: The carbohydrate, identified as mannose, is linked to tryptophan by
an unusual C-glycosidic linkage. The structures determined in NMR and X-ray
diffraction studies differ in assigning the glycosylation as being alpha or
beta, respectively. The beta anomeric form is shown.
synonyms:
- 2'-tryptophan C-mannoside
- (2S)-2-amino-3-(2-beta-D-mannopyranosyl-1H-indol-3-yl)propanoic acid
identifiers:
- ns: go
id: GO:0018103
- ns: pdb.ligand
id: BMA
- ns: resid
id: AA0217
- ns: mod
id: MOD:00222
structure: OC[C@H]1O[C@@H]([C@H]([C@H]([C@@H]1O)O)O)c1[nH]c2c(c1C[C@@H](C(=O)O)[NH3+])cccc2
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 26
l_bond_atoms:
- molecule: Monomer
element: N
position: 29
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 28
- molecule: Monomer
element: H
position: 28
l_displaced_atoms:
- molecule: Monomer
element: H
position: 29
- molecule: Monomer
element: H
position: 29
charge: 1
AA0198:
id: AA0198
name: D-tryptophan
comments: 'Generating Enzyme: protein-tryptophan epimerase (EC 5.1.1.-).'
synonyms:
- (R)-2-amino-3-(1H-indol-3-yl)propanoic acid
- alpha-amino-beta-(3-indolyl)propionoic acid
identifiers:
- ns: resid
id: AA0198
- ns: cas
id: 153-94-6
- ns: go
id: GO:0019128
- ns: pdb.ligand
id: DTR
- ns: chebi
id: CHEBI:29955
- ns: mod
id: MOD:00205
structure: OC(=O)[C@@H](Cc1c[nH]c2c1cccc2)[NH3+]
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
AA0455:
id: AA0455
name: S-palmitoleyl-L-serine
comments: 'Generating Enzyme: protein-serine O-palmitoleyltransferase (EC 2.3.1.-).'
synonyms:
- (2S)-2-amino-3-((9Z)-9-hexadecenoyloxy)propanoic acid
- O3-palmitoleyl-serine
- L-serine cis-9-hexadecenoate ester
identifiers:
- ns: resid
id: AA0455
- ns: mod
id: MOD:01381
- ns: pdb.ligand
id: PAM
structure: CCCCCC/C=C\CCCCCCCC(=O)OC[C@@H](C(=O)O)[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 22
l_bond_atoms:
- molecule: Monomer
element: N
position: 25
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 24
- molecule: Monomer
element: H
position: 24
l_displaced_atoms:
- molecule: Monomer
element: H
position: 25
- molecule: Monomer
element: H
position: 25
charge: 1
AA0338:
id: AA0338
name: N-methyl-L-tyrosine
comments: 'This modification is predicted for proteins homologous to pilin in
certain organisms where the position corresponding to N-methylphenylalanine
instead encodes tyrosine. Polypeptides with monomethylated amino terminals can
undergo premature cleavage during the coupling step of an Edman degradation.
This can result in "preview" with both a residue and the following residue being
seen from the first step on through a sequence. Generating Enzyme: prepilin
peptidase (EC 3.4.23.43).'
synonyms:
- (2S)-3-(4-hydroxyphenyl)-2-methylamino-propanoic acid
- (2S)-3-(4-hydroxyphenyl)-2-(methylamino)propanoic acid
- N-methyltyrosine
- n-methyl-l-tyrosine
- N-methyl-L-tyrosine
identifiers:
- ns: go
id: GO:0046897
- ns: cas
id: 537-49-5
- ns: mod
id: MOD:00343
- ns: pdb-ccd
id: YNM
- ns: resid
id: AA0338
structure: C[NH2+][C@H](C(=O)O)Cc1ccc(cc1)O
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
AA0523:
id: AA0523
name: omega-N,omega-N,omega-N'-trimethyl-L-arginine
comments: No enzyme activities capable of producing this modification under physiological
conditions have been reported.
synonyms:
- N5-[(dimethylamino)(imino)methyl]ornithine
- 2-[(4S)-4-amino-5-oxopentyl]-1,1,3-trimethylguanidine
- N(G)-trimethylarginine
- (2S)-2-amino-5-([(dimethylamino)(methylimino)methyl]amino)pentanoic acid
- (2S)-2-amino-5-([(dimethylamino)(methylamino)methylidene]amino)pentanoic acid
identifiers:
- ns: resid
id: AA0523
- ns: mod
id: MOD:01669
structure: CN/C(=[NH+]/CCC[C@@H](C(=O)O)[NH3+])/N(C)C
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
AA0337:
id: AA0337
name: N-methyl-L-leucine
comments: 'This modification is predicted for proteins homologous to pilin in
certain organisms where the position corresponding to N-methylphenylalanine
instead encodes leucine. Polypeptides with monomethylated amino terminals can
undergo premature cleavage during the coupling step of an Edman degradation.
This can result in "preview" with both a residue and the following residue being
seen from the first step on through a sequence. Generating Enzyme: prepilin
peptidase (EC 3.4.23.43).'
synonyms:
- (S)-2-methylamino-4-methylpentanoic acid
- N-methylleucine
- 2-(methylamino)-4-methyl-valeric acid
- n-methylleucine
- (2S)-4-methyl-2-(methylamino)pentanoic acid
- L
- N-methyl-L-leucine
identifiers:
- ns: pdb.ligand
id: MLE
- ns: pdb-ccd
id: MLE
- ns: cas
id: 3060-46-6
- ns: go
id: GO:0046896
- ns: resid
id: AA0337
- ns: mod
id: MOD:00342
structure: C[NH2+][C@H](C(=O)O)CC(C)C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
AA0582:
id: AA0582
name: 3-methoxydidehydroalanine
comments: It has not been established whether the natural form is the Z or the
E isomer. The Z isomer is shown.
synonyms:
- 2-amino-3-methoxyprop-2-enoic acid
- 3-methoxydidehydroalanine
identifiers:
- ns: mod
id: MOD:01922
- ns: resid
id: AA0582
structure: CO/C=C(/C(=O)O)\N
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
- molecule: Monomer
element: H
position: 7
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
AA0191:
id: AA0191
name: D-alanine
comments: 'Generating Enzyme: protein-alanine epimerase (EC 5.1.1.-).'
synonyms:
- (R)-2-aminopropanoic acid
identifiers:
- ns: resid
id: AA0191
- ns: cas
id: 338-69-2
- ns: mod
id: MOD:00198
- ns: mod
id: MOD:00858
- ns: pdb.ligand
id: DAL
- ns: go
id: GO:0019122
- ns: chebi
id: CHEBI:29949
structure: C[C@@H]([NH3+])C(=O)O
base_monomers:
- A
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
- molecule: Monomer
element: H
position: 4
charge: 1
AA0118:
id: AA0118
name: N6-lipoyl-L-lysine
comments: 'Generating Enzyme: lipoate--protein ligase (EC 6.3.4.-).'
synonyms:
- N6-6,8-dithiooctanoyllysine
- 2-amino-6-(5-[1,2-dithiolan-3-yl]-1-oxopentyl)aminohexanoic acid
- (2S)-2-amino-6-[(5-[(3R)-1,2-dithiolan-3-yl]pentanoyl)amino]hexanoic acid
- (2S)-2-amino-6-(5-[(3R)-1,2-dithiolan-3-yl]pentanamido)hexanoic acid
- N6-lipoyllysine
- (2S,6'R)-2-amino-6-(6,8-dithiooctanamido)hexanoic acid
identifiers:
- ns: resid
id: AA0118
- ns: pdb.ligand
id: LPA
- ns: cas
id: 1200-22-2
- ns: go
id: GO:0018055
- ns: mod
id: MOD:00127
- ns: chebi
id: CHEBI:14919
structure: O=C(CCCC[C@@H]1CCSS1)NCCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 23
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: H
position: 23
- molecule: Monomer
element: H
position: 23
charge: 1
AA0250:
id: AA0250
name: 3-(3'-L-histidyl)-L-tyrosine
comments: The chirality of tyrosine C-3 is not specified; from the model it appears
to be 3R. This modification is different from the modification 3'-(1'-L-histidyl)-L-tyrosine,
see RESID:AA0270.
synonyms:
- 3-(pi-histidyl)tyrosine
- beta-(N3'-histidyl)tyrosine
- (2S,3R)-2-amino-3-(5-[(2S)-2-amino-2-carboxyethyl]-1H-imidazol-1-yl)-3-(4-hydroxyphenyl)propanoic
acid
- 3-(N3'-histidyl)tyrosine
- 3-(pros-histidyl)tyrosine
- beta-(N(delta)-histidyl)tyrosine
identifiers:
- ns: go
id: GO:0018150
- ns: mod
id: MOD:00255
- ns: resid
id: AA0250
structure: O=C[C@H]([C@H](n1cncc1C[C@@H](C(=O)O)[NH3+])c1ccc(cc1)O)N
base_monomers:
- Y
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
- molecule: Monomer
element: H
position: 17
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0584:
id: AA0584
name: O-octanoyl-L-cysteine
comments: 'Generating Enzyme: autocatalytic.'
synonyms:
- (2S)-2-amino-3-(octanoylsulfanyl)propanoic acid
- 2-amino-3-(octanoylthio)propanoic acid
- cysteine octanoate thioester
identifiers:
- ns: mod
id: MOD:01924
- ns: resid
id: AA0584
structure: CCCCCCCC(=O)SC[C@@H](C(=O)O)N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
- molecule: Monomer
element: H
position: 16
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
AA0113:
id: AA0113
name: 3'-(S-L-cysteinyl)-L-tyrosine
comments: In galactose oxidase, cysteinyltyrosine may exist as a stable free radical;
the bond between the sulfur and the phenyl ring appears to have some double
bond character. This modification should not be confused with 3-(S-L-cysteinyl)-L-tyrosine
(see RESID:AA0396).
synonyms:
- S-(tyros-3'-yl)cysteine
- (2S)-2-amino-3-(3-[(2R)2-amino-2-carboxyethylsulfanyl]-4-hydroxyphenyl)propanoic
acid
- 2-amino-3-[3-(2-amino-2-carboxyethylthio)-4-hydroxyphenyl]propanoic acid
- 3'-(cystein-S-yl)tyrosine
identifiers:
- ns: resid
id: AA0113
- ns: mod
id: MOD:00122
- ns: go
id: GO:0018234
structure: O=C[C@H](CSc1cc(ccc1O)C[C@@H](C(=O)O)[NH3+])[NH3+]
base_monomers:
- Y
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
- molecule: Monomer
element: H
position: 19
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
AA0521:
id: AA0521
name: N-(DNA-1',2'-dideoxyribos-1'-ylidene)-L-valine
comments: "The model has three open valences, one on the valine carboxyl group\
\ and two in the DNA nucleotide segment on the 5'-phosphate and the 3'-hydroxyl.\
\ The keyword \"phosphoprotein\" is not used with polynucleotide-linked intermediate\
\ modifications. Generating Enzyme: DNA glycosylase (EC 3.2.2.-)."
synonyms:
- (2S)-2-[(3R,4R)-3,4-dihydroxy-5-(phosphonooxy)pentylidene]amino-3-methylbutanoic
acid
- DNA glycosylase valine Schiff base intermediate
identifiers:
- ns: resid
id: AA0521
- ns: mod
id: MOD:01665
structure: OP(OC[C@H]([C@H](CC[NH2+][C@H](C(=O)O)C(C)C)O)O)O
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
- molecule: Monomer
element: H
position: 18
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
AA0261:
id: AA0261
name: N-L-glutamyl-poly-L-glutamic acid
comments: 'Generating Enzyme: ribosomal S6--glutamic acid ligase (EC 6.3.2.-).'
identifiers:
- ns: mod
id: MOD:00266
- ns: go
id: GO:0018170
- ns: resid
id: AA0261
structure: '[O-]C(=O)CC[C@@H](C(=O)N[C@H](C(=O)[O-])CCC(=O)[O-])[NH3+]'
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
G, Q:
id: AA0189
name: 2-imino-glutamine 5-imidazolinone glycine
comments: 'This entry represents the cross-link of the peptide backbone from the
alpha-carboxyl carbon of residue N, a glutamine, to the alpha-amino nitrogen
of residue N+2, a glycine, coupled with the formation of a double bond to the
alpha-amino nitrogen of residue N, and the loss of a molecule of water. This
cross-link is accompanied by modification of residue N+1. The modified residue
N+1 is presented in a separate entry and is not included in the mass accounting
of this entry. The backbone atoms of residue N+1 are shown in gray in the diagram.
Generating Enzyme: autocatalytic.'
synonyms:
- 2,N-didehydroglutaminyl-5-imidazolinone glycine
- '[2-(4-amino-4-oxobutanimidoyl)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid'
- fluorescent protein FP583 chromophore
- '[2-(3-carbamoyl-1-imino-propyl)-4-(4-hydroxy-benzylidene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic
acid'
- 2-[(4Z)-2-(4-azanyl-4-oxidanylidene-butanimidoyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
- '[(4Z)-2-[(1E)-4-amino-4-oxobutanimidoyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic
acid'
- para-hydroxybenzylidene-imidazolidinone chromophore
- 2-(3-carbamoyl-1-imino-propyl)-1-carboxymethyl-1-imidazolin-5-one
- '[2-(3-carbamoyl-1-imino-propyl)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid'
- QYG
- red fluorescent protein chromophore
identifiers:
- ns: go
id: GO:0019729
- ns: mod
id: MOD:00197
- ns: pdb-ccd
id: CRQ
- ns: pdb.ligand
id: CRQ
- ns: resid
id: AA0189
structure: NC(=O)CCC(=N)C1=NCC(=O)N1CC(=O)O
base_monomers:
- Q
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
- molecule: Monomer
element: H
position: 17
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0269:
id: AA0269
name: L-cysteine persulfide
comments: In desulfurization, the sulfur is donated by free cysteine to peptidyl-cysteine
producing free alanine and peptidyl-cysteine persulfide. See also RESID:AA0101
and RESID:AA0268.
synonyms:
- 3-disulfanylalanine
- 2-amino-3-persulfhydrylpropanoic acid
- S-mercaptocysteine
- (2R)-2-amino-3-disulfanyl-propanoic acid
- 3-disulfanyl-L-alanine
- 2-amino-3-hydrodisulfidopropanoic acid
- s-mercaptocysteine
- C
- S-sulfanylcysteine
- thiocysteine
- 2-amino-3-disulfanylpropanoic acid
- 3-(thiosulfeno)-alanine
- 2-amino-3-hydropersulfidopropanoic acid
- (R)-2-amino-3-disulfanylpropanoic acid
identifiers:
- ns: mod
id: MOD:00274
- ns: pdb-ccd
id: CSS
- ns: go
id: GO:0018179
- ns: chebi
id: CHEBI:61963
- ns: resid
id: AA0269
- ns: pdb.ligand
id: CSS
- ns: cas
id: 5652-32-4
structure: OC(=O)[C@@H]([NH3+])CSS
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
AA0608:
id: AA0608
name: O-(2-acetamido-4-glyceramido-2,4,6-trideoxy-D-glucosyl)-L-serine
comments: The stereochemical identity of the sugar and the glyceryl group have
not been established by chemical methods.
synonyms:
- O-(2-acetamido-4-glyceramido-2,4,6-trideoxy-D-glucopyranosyl)-L-serine
- GATDH
- O-(N2-acetyl-N4-glycerylbacillosaminyl)-L-serine
- (2S)-2-amino-3-[(2-acetamido-4-glycerylamino-2,4,6-trideoxy-D-glucopyranosyl)oxy]propanoic
acid
identifiers:
- ns: mod
id: MOD:01964
- ns: resid
id: AA0608
structure: OC[C@@H](C(=O)N[C@@H]1[C@@H](C)O[C@H]([C@@H]([C@H]1O)NC(=O)C)OC[C@@H](C(=O)O)[NH3+])O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 29
l_bond_atoms:
- molecule: Monomer
element: N
position: 32
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 31
- molecule: Monomer
element: H
position: 31
l_displaced_atoms:
- molecule: Monomer
element: H
position: 32
- molecule: Monomer
element: H
position: 32
charge: 1
K, M:
id: AA0501
name: S-(L-lysyl)-L-methionine sulfilimine
comments: The process for formation of the sulfanylimine bond has not been determined.
It might involve the initial formation of methionine sulfoxide. The lysine involved
in this cross-link in collagen IV is usually hydroxylated, but it is not subsequently
glycosylated.
synonyms:
- (2S)-2-amino-6-([(E)-[(3S)-3-amino-3-carboxypropyl](methyl)-lambda(4)-sulfanylidene]amino)hexanoic
acid
- S-lysyl-methionine
- (E)-N6-([(3S)-3-amino-3-carboxypropyl](methyl)-lambda(4)-sulfanylidene)-L-lysine
identifiers:
- ns: resid
id: AA0501
- ns: mod
id: MOD:01602
structure: O=C[C@H](CCCC/N=[S@](/CC[C@@H](C(=O)O)[NH3+])\C)[NH3+]
base_monomers:
- K
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
- molecule: Monomer
element: H
position: 17
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0527:
id: AA0527
name: N6-octanoyl-L-lysine
comments: 'The metabolic role of this modification is uncertain. Generating Enzyme:
octanoyltransferase (EC 2.3.1.181).'
synonyms:
- (2S)-2-amino-6-(octanoylamino)hexanoic acid
- N6-(1-oxooctyl)-L-lysine
- epsilon-octanoyllysine
- N(zeta)-octanoyllysine
identifiers:
- ns: resid
id: AA0527
- ns: mod
id: MOD:01774
- ns: cas
id: 23735-96-8
structure: CCCCCCCC(=O)NCCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
- molecule: Monomer
element: H
position: 19
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
AA0090:
id: AA0090
name: L-isoleucine amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- isoleucinamide
- (2S,3S)-2-amino-3-methylpentanamide
identifiers:
- ns: cas
id: 14445-54-6
- ns: chebi
id: CHEBI:21345
- ns: resid
id: AA0090
- ns: mod
id: MOD:00099
- ns: go
id: GO:0018043
- ns: pdb.ligand
id: NH2
structure: CC[C@@H]([C@@H](C(=O)N)[NH3+])C
base_monomers:
- I
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
H, M:
id: AA0566
name: N-[(L-histidin-1'-yl)methyl]-L-methionine
comments: 'The electron density model has contradictory characteristics. The bond
distances from the "formyl" carbon to the two nitrogens are in the single bond
range, and the torsion angles around those bonds are not planar, suggesting
that neither is a double bond. However, the bond angle between that carbon and
the two nitrogens is closer to trigonal than to tetrahedral, suggesting sp2
hybridization. The modification is shown in a reduced state. Since both the
source organism and the expression host encode N-formylmethionine initiator
and the autocatalytic modification can occur before completion of translation,
it is probable but not yet established that the modification occurs under natural
conditions. Generating Enzyme: autocatalytic.'
synonyms:
- (2S)-2-([(4-[(2S)-2-amino-2-carboxyethyl]-1H-imidazol-1-yl)methyl]amino)-4-(methylsulfanyl)butanoic
acid
identifiers:
- ns: pdb.ligand
id: FME
- ns: mod
id: MOD:01890
- ns: mod
id: MOD:01891
- ns: resid
id: AA0566
structure: CSCC[C@@H](C(=O)O)NCn1cnc(c1)C[C@@H](C=O)[NH3+]
base_monomers:
- AA0021
- M
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
AA0399:
id: AA0399
name: O-(N-acetylaminoglucosyl)-L-threonine
comments: 'See also RESID:AA0155, RESID:AA0247, RESID:AA0401, RESID:AA0403, RESID:AA0405,
and RESID:AA0515 for other O-glycosylated threonines. The PDB has some entries
with threonine apparently alpha-glycosylated with N-acetylglucosamine. These
are low resolution structures and appear to be erroneous. Generating Enzyme:
[protein]-L-serine/L-threonine beta-N-acetyl-D-glucosaminyl-transferase (EC
2.4.1.-).'
synonyms:
- O-threonyl-beta-N-acetylglucosaminide
- O3-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-L-threonine
- O3-(N-acetylglucosaminyl)threonine
- O-glycosylthreonine
- O-(2-acetylamino-2-deoxy-beta-D-glucopyranosyl)-L-threonine
- (2S,3R)-2-amino-3-(2-acetamido-2-deoxy-beta-D-glucopyranosyloxy)butanoic acid
- O-(N-acetylglucosaminyl)-L-threonine
identifiers:
- ns: mod
id: MOD:00806
- ns: cas
id: 10036-64-3
- ns: pdb.ligand
id: NDG
- ns: resid
id: AA0399
structure: OC[C@H]1O[C@@H](O[C@@H]([C@@H](C(=O)O)[NH3+])C)[C@@H]([C@H]([C@@H]1O)O)NC(=O)C
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0486:
id: AA0486
name: 1-amino-2-propanone
synonyms:
- aminoacetone
- 1-aminopropan-2-one
- 1-aminopropanone
identifiers:
- ns: mod
id: MOD:01433
- ns: cas
id: 298-08-8
- ns: chebi
id: CHEBI:17906
- ns: resid
id: AA0486
structure: CC(=O)C[NH3+]
base_monomers:
- T
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
AA0433:
id: AA0433
name: N,N-dimethyl-L-alanine
comments: 'Generating Enzyme: ribosomal protein L11 methyltransferase prmA (EC
2.1.1.-); N-terminal RCC1 methyltransferase (EC 2.1.1.-).'
synonyms:
- (S)-2-(dimethylamino)propanoic acid
- N,N-dimethyl-L-alanine
- (2S)-2-dimethylaminopropanoic acid
- n,n-dimethyl-l-alanine
- (S)-1-carboxy-N,N-dimethylaminoethane
- N,N-dimethylalanine
- A
identifiers:
- ns: resid
id: AA0433
- ns: cas
id: 2812-31-9
- ns: mod
id: MOD:01179
- ns: pdb-ccd
id: LAL
- ns: go
id: GO:0018011
structure: C[C@@H](C(=O)O)[NH+](C)C
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
- molecule: Monomer
element: H
position: 6
AA0251:
id: AA0251
name: L-methionine sulfone
synonyms:
- (2S)-2-amino-4-methylsulfonyl-butanoic acid
- S,S-dioxymethionine
- L-methionine S,S-dioxide
- (2S)-2-amino-4-(methylsulfonyl)butanoic acid
- M
- s-dioxymethionine
identifiers:
- ns: cas
id: 7314-32-1
- ns: resid
id: AA0251
- ns: mod
id: MOD:00256
- ns: pdb-ccd
id: OMT
- ns: go
id: GO:0018159
- ns: pdb.ligand
id: OMT
structure: OC(=O)[C@H](CCS(=O)(=O)C)[NH3+]
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
AA0443:
id: AA0443
name: (2S,4R)-5-hydroxyleucine
comments: The oxidation artifacts 5-hydroxyleucine and 5-oxoleucine can form autocatalytically
and stereospecifically, but not selectively. It is not clear whether the modified
residue subsequently takes part in catalytic reactions at the active site of
alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 (ABH3).
synonyms:
- delta-hydroxyleucine
- (4R)-5-hydroxyleucine
- (2S,4R)-2-amino-5-hydroxy-4-methylpentanoic acid
- (2~{S},4~{R})-2-azanyl-4-methyl-5-oxidanyl-pentanoic acid
- L
- (2s,4r)-5-hydroxyleucine
identifiers:
- ns: pdb-ccd
id: HL5
- ns: mod
id: MOD:01373
- ns: resid
id: AA0443
structure: OC[C@@H](C[C@@H](C(=O)O)[NH3+])C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
AA0171:
id: AA0171
name: S-sulfo-L-cysteine
synonyms:
- cysteine-S-sulfonic acid
- 3-(sulfosulfanyl)-L-alanine
- (2R)-2-amino-3-(sulfosulfanyl)propanoic acid
- cysteine-s-sulfonic acid
- C
- S-sulfocysteine
- 2-amino-3-(sulfothio)propanoic acid
- (2R)-2-amino-3-sulfosulfanyl-propanoic acid
- cysteine sulfate thioester
identifiers:
- ns: mod
id: MOD:00180
- ns: go
id: GO:0018248
- ns: chebi
id: CHEBI:27891
- ns: resid
id: AA0171
- ns: pdb-ccd
id: CSU
- ns: cas
id: 1637-71-4
- ns: pdb.ligand
id: CSU
structure: OC(=O)[C@H](CSS(O)(O)O)N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
AA0049:
id: AA0049
name: N-acetyl-L-methionine
comments: 'Although appropriate, the keyword "thioether bond" normally does not
appear for this amino acid. Generating Enzyme: peptide alpha-N-acetyltransferase
(EC 2.3.1.88).'
synonyms:
- 2-acetylamino-4-(methylthio)butanoic acid
- methionamine
- (2S)-2-acetamido-4-(methylsulfanyl)butanoic acid
- 2-acetylamino-4-(methylsulfanyl)butanoic acid
- acetylmethionine
- 2-acetylazanyl-4-(methylsulfanyl)butanoic acid
identifiers:
- ns: cas
id: 65-82-7
- ns: chebi
id: CHEBI:21557
- ns: go
id: GO:0017196
- ns: resid
id: AA0049
- ns: mod
id: MOD:00058
structure: CSCC[C@@H](C(=O)O)NC(=O)C
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
AA0211:
id: AA0211
name: N6-formyl-L-lysine
synonyms:
- (2S)-2-amino-6-(formylamino)hexanoic acid
- N(zeta)-formyllysine
- epsilon-formyllysine
identifiers:
- ns: cas
id: 1190-48-3
- ns: resid
id: AA0211
- ns: go
id: GO:0018257
- ns: mod
id: MOD:00216
structure: O=CNCCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
AA0500:
id: AA0500
name: 3'-farnesyl-2',3'-dihydro-2',N2-cyclo-L-tryptophan
synonyms:
- (2S,3aR,8aS)-3a-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]-1,2,3,3a,8,8a-hexahydropyrrolo[2,3-b]indole-2-carboxylic
acid
identifiers:
- ns: resid
id: AA0500
- ns: chebi
id: CHEBI:52950
- ns: mod
id: MOD:01590
structure: C/C(=C\C[C@]12C[C@H](N[C@H]1Nc1c2cccc1)C(=O)O)/CC/C=C(/CCC=C(C)C)\C
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 19
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 21
- molecule: Monomer
element: H
position: 21
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
AA0358:
id: AA0358
name: L-cysteinyl-L-selenocysteine
comments: The experimental redox potential of cysteinylselenocysteine in synthetic
glutaredoxin 3 is -260 to -275 mV. See RESID:AA0025 and RESID:AA0437.
synonyms:
- (R,R)-2-amino-3-[3-(2-aminopropanoic acid)sulfanyl]selanylpropanoic acid
identifiers:
- ns: resid
id: AA0358
- ns: mod
id: MOD:00867
- ns: mod
id: MOD:00363
- ns: go
id: GO:0050837
structure: O=C[C@H](CS[Se]C[C@@H](C(=O)O)N)[NH3+]
base_monomers:
- C
- U
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
AA0221:
id: AA0221
name: 1'-(8alpha-FAD)-L-histidine
comments: 'The arrangement of the attachment has not been completely established
in some cases. The keyword "phosphoprotein" is not used with flavin modifications
linked through the flavin. Generating Enzyme: apo mitochondrial succinate dehydrogenase
[ubiquinone] flavoprotein subunit---FAD ligase sdh5 (EC 6.3.4.-).'
synonyms:
- (S)-2-amino-3-(1-[8alpha riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester
with adenosine]imidazol-4-yl)propanoic acid
- N(tau)-(8alpha-FAD)-histidine
- 8alpha-(N(epsilon)-histidyl)FAD
- tele-(8alpha-FAD)-histidine
- 8alpha-N3-histidyl FAD [misnomer]
- 8alpha-(N1'-histidyl)FAD
identifiers:
- ns: resid
id: AA0221
- ns: pdb.ligand
id: FAD
- ns: go
id: GO:0018297
- ns: mod
id: MOD:00226
structure: O=c1[nH]c(=O)c2c([nH]1)n(C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O[P@@](=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc3c1NC=N[C@H]3N)[O-])[O-])O)O)O)c1=C[C@H](C(=Cc1[nH+]2)C)Cn1cnc(c1)C[C@@H](C(=O)O)[NH3+]
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 74
l_bond_atoms:
- molecule: Monomer
element: N
position: 77
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 76
- molecule: Monomer
element: H
position: 76
l_displaced_atoms:
- molecule: Monomer
element: H
position: 77
- molecule: Monomer
element: H
position: 77
charge: 1
AA0028:
id: AA0028
name: 5-hydroxy-L-lysine
comments: 'Some forms of lysyl hydroxylase are multifunctional and possess both
galactosyltransferase (EC 2.4.1.50) and glucosyltransferase (EC 2.4.1.66) activities.
Generating Enzyme: procollagen-lysine 5-dioxygenase (EC 1.14.11.4).'
synonyms:
- 2,6-diamino-2,3,4,6-tetradeoxyhexonic acid
- L-erythro-delta-hydroxylysine
- alpha,epsilon-diamino-delta-hydroxycaproic acid
- 2,6-bisazanyl-5-hydroxyhexanoic acid
- (5R)-5-hydroxy-L-lysine
- (2S,5R)-2,6-diamino-5-hydroxy-hexanoic acid
- K
- 5-hydroxylysine
- (2S,5R)-2,6-diamino-5-hydroxyhexanoic acid
identifiers:
- ns: resid
id: AA0028
- ns: pdb-ccd
id: LYZ
- ns: go
id: GO:0018395
- ns: mod
id: MOD:00037
- ns: chebi
id: CHEBI:18040
- ns: cas
id: 1190-94-9
- ns: pdb.ligand
id: LYZ
structure: '[NH3+]C[C@@H](CC[C@@H](C(=O)O)[NH3+])O'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
W, W:
id: AA0544
name: 1-(L-tryptophan-3-yl)-L-tryptophan
comments: 'The production of this cross-link during bicarbonate-dependent peroxidase
catalysis may be artifactual. Generating Enzyme: autocatalytic.'
synonyms:
- 3-[(2S)-2-amino-2-carboxyethyl]-3-(3-[(2S)-2-amino-2-carboxyethyl]-1H-indol-2-yl)-1H-indole
- (2S,2'S)-3,3'-(3'H-1,3'-biindole-3,3'-diyl)bis(2-aminopropanoic acid)
- 3-[2-azanyl-2-carboxyethyl]-3-(3-[2-azanyl-2-carboxyethyl]-1H-indol-2-yl)-1H-indole
- ditryptophan
- 2-amino-3-[2-[2-amino-3-(2-carboxyethyl)-1H-indol-4-yl]-1H-indol-3-yl]propanoic
acid
identifiers:
- ns: resid
id: AA0544
- ns: mod
id: MOD:01818
structure: O=C[C@H](Cc1cn(c2c1cccc2)[C@@]1(C=Nc2c1cccc2)C[C@@H](C(=O)O)[NH3+])[NH3+]
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 27
l_bond_atoms:
- molecule: Monomer
element: N
position: 30
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 29
- molecule: Monomer
element: H
position: 29
l_displaced_atoms:
- molecule: Monomer
element: H
position: 30
- molecule: Monomer
element: H
position: 30
charge: 1
AA0381:
id: AA0381
name: L-lysine 5-imidazolinone glycine
comments: 'This entry represents the cross-link of the peptide backbone from the
alpha-carboxyl carbon of residue N, a lysine, to the alpha-amino nitrogen of
residue N+2, a glycine, coupled with the formation of a double bond to the alpha-amino
nitrogen of residue N+1 which loses one hydrogen, and the loss of a molecule
of water. This cross-link is accompanied by modification of residue N+1. The
modified residue N+1 is presented in a separate entry and is not included in
the mass accounting of this entry. The backbone atoms of residue N+1 are shown
in gray in the diagram. Generating Enzyme: autocatalytic.'
synonyms:
- '{(4Z)-2-[(1S)-1,5-diaminopentyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid'
- lysyl-5-imidazolinone glycine
- 2-[(4Z)-2-[(1S)-1,5-diaminopentyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-imidazol-1-yl]ethanoic
acid
- '[2-(1,5-diaminopentanyl)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid'
- 2-[(S)-1,5-diaminopentanyl]-1-carboxymethyl-1-imidazolin-5-one
- para-hydroxybenzylidene-imidazolidinone chromophore
- Anemonia majano fluorescent protein FP486 chromophore
- KYG
- (2-[(1S)-1,5-diaminopentyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl)acetic acid
- '[(4z)-2-[(1s)-1,5-diaminopentyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic
acid'
identifiers:
- ns: pdb-ccd
id: CR7
- ns: resid
id: AA0381
- ns: mod
id: MOD:00386
- ns: go
id: GO:0051361
- ns: pdb.ligand
id: CR7
structure: '[NH3+]CCCC[C@@H](C1=NCC(=O)N1CC(=O)O)[NH3+]'
base_monomers:
- K
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
- molecule: Monomer
element: H
position: 20
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AA0057:
id: AA0057
name: N-formylglycine
comments: This modification should not be confused with L-3-oxoalanine, also referred
to as C(alpha)-formylglycine (see RESID:AA0185).
synonyms:
- (formylamino)ethanoic acid
- (formylamino)acetic acid
- N(alpha)-formylglycine
- 2-formamidoethanoic acid
- 2-formamidoacetic acid
- (formylazanyl)ethanoic acid
identifiers:
- ns: chebi
id: CHEBI:21717
- ns: cas
id: 2491-15-8
- ns: mod
id: MOD:00066
- ns: go
id: GO:0018005
- ns: resid
id: AA0057
structure: O=CNCC(=O)O
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 3
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
- molecule: Monomer
element: H
position: 7
l_displaced_atoms:
- molecule: Monomer
element: H
position: 3
AA0282:
id: AA0282
name: (2S,3R,4S)-3,4-dihydroxyproline
synonyms:
- (2S,3R,4S)-3,4-dihydroxypyrrolidine-2-carboxylic acid
- trans-2,3-cis-3,4-dihydroxy-L-proline
- 2-alpha-3-beta-4-beta-3,4-dihydroxyproline
- 2,3-trans-3,4-cis-3,4-dihydroxy-L-proline
identifiers:
- ns: mod
id: MOD:00287
- ns: cas
id: 95341-64-3
- ns: resid
id: AA0282
- ns: go
id: GO:0018188
structure: O[C@H]1C[NH2+][C@@H]([C@H]1O)C(=O)O
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
AA0520:
id: AA0520
name: 7'-hydroxy-L-tryptophan
comments: "This modification without secondary glycosylation (see RESID:AA0506)\
\ has only been observed as the first precursor form of 4'-(L-tryptophan)-L-tryptophyl\
\ quinone (see RESID:AA0149). Generating Enzyme: peptidyl-tryptophan 7-oxygenase\
\ MauX (EC 1.-.-.-)."
synonyms:
- 7-hydroxy-l-tryptophan
- W
- (2S)-2-amino-3-(7-hydroxy-1H-indol-3-yl)propanoic acid
- 7-hydroxy-L-tryptophan
identifiers:
- ns: pdb.ligand
id: 0AF
- ns: pdb-ccd
id: 0AF
- ns: resid
id: AA0520
- ns: mod
id: MOD:01664
structure: OC(=O)[C@H](Cc1c[nH]c2c1cccc2O)[NH3+]
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0382:
id: AA0382
name: 2-tetrahydropyridinyl-5-imidazolinone glycine
comments: 'This entry represents the cross-link of the peptide backbone from the
alpha-carboxyl carbon of residue N, a lysine, to the alpha-amino nitrogen of
residue N+2, a glycine, coupled with the formation of a double bond to the alpha-amino
nitrogen of residue N+1 which loses one hydrogen, and the loss of a molecule
of water. In addition, the residue N lysine undergoes cyclization. The alpha-amino
nitrogen is replaced by the epsilon-amino nitrogen, the peptide chain is broken,
residue N-1 is released as an amide, and a double bond is formed between the
alpha-carbon and the nitrogen so that a tetrahydropyridine ring results. This
cross-link is accompanied by modification of residue N+1. The modified residue
N+1 is presented in a separate entry and is not included in the mass accounting
of this entry. The backbone atoms of residue N+1 are shown in gray in the diagram.
Generating Enzyme: autocatalytic.'
synonyms:
- 2-[(4Z)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-2-(3,4,5,6-tetrahydropyridin-2-yl)imidazol-1-yl]ethanoic
acid
- '[5-oxo-2-(3,4,5,6-tetrahydropyridin-2-yl)-4,5-dihydro-1H-imidazol-1-yl]acetic
acid'
- '[(4z)-4-(4-hydroxybenzylidene)-5-oxo-2-(3,4,5,6-tetrahydropyridin-2-yl)-4,5-dihydro-1h-imidazol-1-yl]acetic
acid'
- Zoanthus sp. fluorescent protein zFP538 chromophore
- para-hydroxybenzylidene-imidazolidinone chromophore
- 2-(3,4,5,6-tetrahydropyridin-2-yl)-1-carboxymethyl-1-imidazolin-5-one
- '[(4Z)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-2-(3,4,5,6-tetrahydropyridin-2-yl)-4,5-dihydro-1H-imidazol-1-yl]acetic
acid'
- KYG
- 2-(tetrahydropyrid-2-yl)-5-imidazolinone glycine
identifiers:
- ns: pdb.ligand
id: CH7
- ns: resid
id: AA0382
- ns: pdb-ccd
id: CH7
- ns: mod
id: MOD:00387
- ns: go
id: GO:0051362
structure: OC(=O)CN1C(=O)CN=C1[C@@H]1CCCC[NH2+]1
base_monomers:
- K
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
AA0051:
id: AA0051
name: N-acetyl-L-serine
comments: 'Generating Enzyme: peptide alpha-N-acetyltransferase (EC 2.3.1.88).'
synonyms:
- N-acetyl-L-serine
- N-acetylserine
- 2-acetylazanyl-3-hydroxypropanoic acid
- (2S)-2-acetamido-3-hydroxy-propanoic acid
- (2S)-2-acetamido-3-hydroxypropanoic acid
- 2-acetylamino-3-hydroxypropanoic acid
- S
- n-acetyl-serine
identifiers:
- ns: resid
id: AA0051
- ns: go
id: GO:0017198
- ns: pdb-ccd
id: SAC
- ns: chebi
id: CHEBI:45441
- ns: cas
id: 16354-58-8
- ns: mod
id: MOD:00060
structure: OC[C@@H](C(=O)O)NC(=O)C
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
- molecule: Monomer
element: H
position: 7
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
AA0127:
id: AA0127
name: pyruvic acid
comments: The pyruvic acid forming an amide bond between its 1-carboxyl group
and an amino terminal residue arises from oxidative deamination of an encoded
amino acid, either cysteine or serine. It is important to distinguish this modification
from an exogenous pyruvic acid forming a ketimine bond with its 2-keto group
and an amino terminal residue (see RESID:AA0274 and RESID:AA0275).
synonyms:
- 2-oxopropanoic acid
identifiers:
- ns: pdb.ligand
id: PYR
- ns: resid
id: AA0127
- ns: mod
id: MOD:00807
- ns: cas
id: 127-17-3
- ns: go
id: GO:0018058
- ns: mod
id: MOD:01661
- ns: mod
id: MOD:00136
structure: OC(=O)C(=O)C
base_monomers:
- S
- Y
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
AA0392:
id: AA0392
name: S-galactosyl-L-cysteine
comments: The beta form is shown. See also RESID:AA0152 and RESID:AA0560 for other
S-glycosylated cysteines.
synonyms:
- (2R)-2-amino-3-(D-galactopyranosylsulfanyl)propanoic acid
- S-(beta-D-galactopyranosyl)cysteine
- S-glycosyl-cysteine
identifiers:
- ns: mod
id: MOD:00799
- ns: resid
id: AA0392
structure: OC[C@H]1O[C@@H](SC[C@@H](C(=O)O)[NH3+])[C@@H]([C@H]([C@H]1O)O)O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0203:
id: AA0203
name: O4'-(phospho-5'-adenosine)-L-tyrosine
synonyms:
- (2S)-2-amino-3-[4-(5'-adenosine phosphonoxy)phenyl]propanoic acid
- hydrogen 5'-adenylate tyrosine ester
- O4'-L-tyrosine 5'-adenosine phosphodiester
- 5'-adenylic-O-tyrosine
identifiers:
- ns: pdb.ligand
id: AMP
- ns: cas
id: 93957-03-0
- ns: resid
id: AA0203
- ns: go
id: GO:0018254
- ns: mod
id: MOD:00208
structure: OC(=O)[C@H](Cc1ccc(cc1)OP(=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)[O-])[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 40
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 40
- molecule: Monomer
element: H
position: 40
charge: 1
AA0506:
id: AA0506
name: 7'-hydroxy-2'-alpha-mannosyl-L-tryptophan
comments: The 7'-hydroxylation of tryptophan apparently makes it susceptible to
oxidation and cross-linking, however these secondary products have not been
characterized.
synonyms:
- (2S)-2-amino-3-[7-hydroxy-2-(alpha-D-mannopyranosyl)-1H-indol-3-yl]propanoic
acid
identifiers:
- ns: mod
id: MOD:01609
- ns: resid
id: AA0506
structure: OC[C@H]1O[C@@H]([C@H]([C@H]([C@@H]1O)O)O)c1[nH]c2c(c1C[C@@H](C(=O)O)[NH3+])cccc2O
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 26
l_bond_atoms:
- molecule: Monomer
element: N
position: 29
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 28
- molecule: Monomer
element: H
position: 28
l_displaced_atoms:
- molecule: Monomer
element: H
position: 29
- molecule: Monomer
element: H
position: 29
charge: 1
AA0489:
id: AA0489
name: '[cyclo(prolylserin)-O-yl] cysteinate'
comments: This diketopiperazine ester is formed by cyclization of the C-terminal
seryl-proline dipeptide and transesterification to cysteine. Although it is
constructed from three C-terminal amino acids, for simplicity it is represented
in the UniProt feature as a modification of cysteine and not as a crosslink.
synonyms:
- (3,6-dioxopyrrolo[4,5-a]piperazin-2-yl)methyl cysteinate
- '[(3S,8aS)-1,4-dioxooctahydropyrrolo[1,2-a]pyrazin-3-yl]methyl (2R)-2-amino-3-sulfanylpropanoate'
identifiers:
- ns: resid
id: AA0489
- ns: mod
id: MOD:01436
- ns: mod
id: MOD:01437
structure: SC[C@@H](C(=O)OC[C@@H]1NC(=O)[C@H]2N(C1=O)CCC2)N
base_monomers:
- P
- S
- C
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
AA0066:
id: AA0066
name: N,N-dimethyl-L-proline
comments: 'Consult FAQ at http://pir.georgetown.edu/resid/faq.shtml#q12 concerning
calculation of the difference formula. Generating Enzyme: N-terminal RCC1 methyltransferase
(EC 2.1.1.-).'
synonyms:
- stachydrin
- (2S)-2-carboxy-1,1-dimethylpyrrolidinium
- 1,1-dimethyl-L-prolinium
- N,N-dimethyl-L-prolinium
identifiers:
- ns: go
id: GO:0018016
- ns: cas
id: 51705-67-0
- ns: mod
id: MOD:00075
- ns: pdb.ligand
id: PBE
- ns: chebi
id: CHEBI:21451
- ns: resid
id: AA0066
structure: OC(=O)[C@@H]1CCC[N]1(C)C
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
AA0373:
id: AA0373
name: L-aspartyl aldehyde
synonyms:
- L-aspartic beta-semialdehyde
- L-aminosuccinic acid semialdehyde
- L-beta-formylalanine
- (S)-2-amino-4-oxobutanoic acid
- L-aminosuccinaldehydic acid
- L-aspartate-beta-semialdehyde
identifiers:
- ns: go
id: GO:0051203
- ns: mod
id: MOD:00378
- ns: resid
id: AA0373
- ns: cas
id: 498-20-4
structure: O=CC[C@@H](C(=O)O)[NH3+]
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
- molecule: Monomer
element: H
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
AA0508:
id: AA0508
name: 6-(S-L-cysteinyl)-8alpha-(N3'-L-histidino)-FMN
comments: 'The keyword "phosphoprotein" is not used with flavin modifications
linked through the flavin. Generating Enzyme: autocatalytic.'
synonyms:
- 6-(S-cysteinyl)-8alpha-(N(pi)-histidyl)-FMN
- 6-((R)-2-amino-2-carboxyethyl)sulfanyl-8alpha-[4-((S)-2-amino-2-carboxyethyl)imidazol-3-yl]-riboflavin
5'-trihydrogen phosphate
- 6-(S-cysteinyl)-8alpha-(pros-histidyl)-FMN
- 6-(S-cysteinyl)-8alpha-(N(delta)-histidyl)-FMN
- 6-(S-cysteinyl)-8alpha-(N3'-histidyl)-FMN
identifiers:
- ns: mod
id: MOD:01611
- ns: resid
id: AA0508
structure: O=C[C@H](CS[C@@H]1C(=C(C=C2C1=N[C@@H]1C(=O)NC(=O)N=C1N2C[C@@H]([C@@H]([C@@H](COP(=O)([O-])[O-])O)O)O)Cn1cncc1C[C@@H](C(=O)O)[NH3+])C)[NH3+]
base_monomers:
- C
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 50
l_bond_atoms:
- molecule: Monomer
element: N
position: 53
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 52
- molecule: Monomer
element: H
position: 52
l_displaced_atoms:
- molecule: Monomer
element: H
position: 53
- molecule: Monomer
element: H
position: 53
charge: 1
AA0199:
id: AA0199
name: D-threonine
comments: 'Generating Enzyme: protein-threonine 2-epimerase (EC 5.1.1.-).'
synonyms:
- (2R,3R)-2-amino-3-hydroxybutanoic acid
identifiers:
- ns: mod
id: MOD:00863
- ns: chebi
id: CHEBI:32826
- ns: cas
id: 632-20-2
- ns: pdb.ligand
id: DTH
- ns: resid
id: AA0199
structure: C[C@H]([C@H](C(=O)O)[NH3+])O
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
- molecule: Monomer
element: H
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
AA0041:
id: AA0041
name: N-acetyl-L-alanine
comments: 'Generating Enzyme: peptide alpha-N-acetyltransferase (EC 2.3.1.88);
ribosomal-protein-alanine N-acetyltransferase (EC 2.3.1.128).'
synonyms:
- (2S)-2-acetamidopropanoic acid
- 2-(acetylazanyl)propanoic acid
- 2-(acetylamino)propanoic acid
- N-acetyl-L-alanine
- n-acetylalanine
- (2S)-2-(acetamido)propanoic acid
- A
- acetylalanine
identifiers:
- ns: go
id: GO:0017189
- ns: mod
id: MOD:00050
- ns: pdb-ccd
id: AYA
- ns: chebi
id: CHEBI:61920
- ns: resid
id: AA0041
- ns: cas
id: 97-69-8
structure: CC(=O)N[C@H](C(=O)O)C
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
AA0040:
id: AA0040
name: 2'-[3-carboxamido-3-(trimethylammonio)propyl]-L-histidine
comments: 'Diphthamide appears to occur uniquely in translation elongation factor
eEF-2. Generating Enzyme: diphthine synthase Dph5 (EC 2.1.1.98); diphthine--ammonia
ligase (EC 6.3.2.22); diphthamide biosynthesis protein, histidine 3-carboxy-3-aminopropyltransferase
(EC 2.5.1.-).'
synonyms:
- (2R)-1-amino-4-{4-[(2S)-2-amino-2-carboxyethyl]-1H-imidazol-2-yl}-N,N,N-trimethyl-1-oxobutan-2-aminium
- (2R)-1-amino-4-(4-[(2S)-2-amino-2-carboxyethyl]-1H-imidazol-2-yl)-N,N,N-trimethyl-1-oxobutan-2-aminium
- 2-amino-3-[[2-(3-amino-3-carbamoyl-prop-1-enyl)-1,1,3-trimethyl-2,3-dihydroimidazol-5-yl]]propanoic
acid
- alpha-(aminocarbonyl)-4-(2-amino-2-carboxyethyl)-N,N,N-trimethyl-1H-imidazole-2-propanaminium
- 2-amino-4-[[5-(2-amino-2-carboxylato-ethyl)-1,1,3-trimethyl-2,3-dihydroimidazol-2-yl]]but-3-enamide
- 2-[3-carboxamido-3-(trimethylammonio)propyl]histidine
- '[(2R)-1-amino-4-[4-[(2S)-2-amino-3-hydroxy-3-oxo-propyl]-1H-imidazol-2-yl]-1-oxo-butan-2-yl]-trimethyl-azanium'
- H
- diphthamide
- 2-[(R)-3-carboxamido-3-(trimethylammonio)propyl]-4-((S)-2-amino-2-carboxyethyl)-1H-imidazole
- (3-[4-(2-amino-2-carboxy-ethyl)-1H-imidazol-2-yl]-1-carbamoyl-propyl)-trimethylammonium
- '{3-[4-(2-amino-2-carboxy-ethyl)-1h-imidazol-2-yl]-1-carbamoyl-propyl}-trimethyl-ammonium'
- 1-azanyl-4-(4-[2-azanyl-2-carboxyethyl]-1H-imidazol-2-yl)-N,N,N-trimethyl-1-oxobutan-2-azanium
identifiers:
- ns: go
id: GO:0006471
- ns: pdb.ligand
id: DDE
- ns: resid
id: AA0040
- ns: cas
id: 75645-22-6
- ns: chebi
id: CHEBI:16692
- ns: mod
id: MOD:00049
- ns: pdb-ccd
id: DDE
structure: N[C@H](C(=O)O)Cc1c[nH]c(n1)CC[C@@H]([N](C)(C)C)C(=O)N
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0561:
id: AA0561
name: S-(2-succinyl)-L-cysteine
comments: 'This modification is produced in the active site inhibition of glyceraldehyde-3-phosphate
dehydrogenase by fumarate, but as the active site intermediate in maleate isomerase.
Generating Enzyme: autocatalytic.'
synonyms:
- (2R)-2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}butanedioic acid
- 2-amino-3-(1,2-dicarboxyethylthio)propanoic acid
- S-(2-succinyl)cysteine
- (2R)-2-amino-3-([(1R)-1,2-dicarboxyethyl]sulfanyl)propanoic acid
- 2-((2-amino-2-carboxyethyl)thio)butanedioic acid
- S-[(2R)-2-succinyl]-L-cysteine
- S-(1,2-dicarboxyethyl)cysteine
identifiers:
- ns: mod
id: MOD:01889
- ns: pdb.ligand
id: SIN
- ns: cas
id: 34317-60-7
- ns: resid
id: AA0561
structure: O=C[C@H](CS[C@@H](C(=O)[O-])CC(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0400:
id: AA0400
name: O-galactosyl-L-serine
comments: 'See also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291,
RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0402, RESID:AA0404,
RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines. Generating
Enzyme: galactosyltransferase (EC 2.4.1.-).'
synonyms:
- (2S)-2-amino-3-(alpha-D-galactopyranosyloxy)propanoic acid
- O3-galactosylserine
- O-glycosylserine
identifiers:
- ns: resid
id: AA0400
- ns: mod
id: MOD:00808
structure: OC[C@H]1O[C@H](OC[C@@H](C(=O)O)[NH3+])[C@@H]([C@H]([C@H]1O)O)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0617:
id: AA0617
name: S-(poly-3-hydroxybutyrate)-L-cysteine
comments: 'The mechanism of biosynthesis may involve transfer of the polymer to
and from a noncovalently bound coenzyme A. The intermediate modification with
two polymeric units is presented. Generating Enzyme: autocatalytic.'
synonyms:
- S-poly[(R)-3-hydroxybutyrate]cysteine
- S-poly(3-hydroxybutanoic acid)cysteine
- (alpha)-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-(omega)-[(3R)-3-hydroxybutanoyl]-poly([(3R)-3-methyl-1-oxopropane-1,3-diyl]oxy)
- S-poly(3-hydroxybutanoate)cysteine
- S-poly(beta-hydroxybutyrate)cysteine
- S-poly(3-hydroxybutyrate)cysteine
- S-poly(3-hydroxybutyric acid)cysteine
identifiers:
- ns: cas
id: 29435-48-1
- ns: mod
id: MOD:01975
- ns: resid
id: AA0617
structure: C[C@H](CC(=O)O[C@@H](CC(=O)SC[C@@H](C(=O)O)N)C)O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
- molecule: Monomer
element: H
position: 19
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
AA0512:
id: AA0512
name: glycyl cysteine dithioester
comments: These are highly reactive dithioester cross-links formed between internal
cysteine residues of ThiF and the carboxyl end of ThiS and other similar proteins.
synonyms:
- S-glycyl thiocysteine
- S-glycyl cysteine persulfide
- 2-(glycyldithio)alanine
- (2R)-2-amino-3-[(aminoacetyl)disulfanyl]propanoic acid
- thioglycine cysteine disulfide
identifiers:
- ns: mod
id: MOD:01615
- ns: resid
id: AA0512
structure: OC(=O)[C@@H]([NH3+])CSSC(=O)C[NH3+]
base_monomers:
- C
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
AA0317:
id: AA0317
name: 1'-methyl-L-histidine
comments: 'In the older biochemical literature this is usually called 3-methylhistidine.
See also RESID:AA0073. The crystallographic designation for the substituted
nitrogen is epsilon-2, E2. Generating Enzyme: protein-histidine N-methyltransferase
(EC 2.1.1.85).'
synonyms:
- tele-methylhistidine
- 1-methyl-L-histidine
- 4-methyl-histidine
- 3-methylhistidine [misnomer]
- H
- (S)-2-amino-3-(1-methyl-1H-imidazol-4-yl)propanoic acid
- (2S)-2-amino-3-(1-methylimidazol-4-yl)propanoic acid
- 4-methyl-histidine [misnomer]
- N(tau)-methylhistidine
- N(epsilon)-methylhistidine
identifiers:
- ns: mod
id: MOD:00322
- ns: pdb-ccd
id: HIC
- ns: cas
id: 332-80-9
- ns: resid
id: AA0317
- ns: chebi
id: CHEBI:16367
- ns: go
id: GO:0018021
- ns: pdb.ligand
id: HIC
structure: Cn1cc(nc1)C[C@H]([NH3+])C(=O)O
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
- molecule: Monomer
element: H
position: 16
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
AA0449:
id: AA0449
name: (3R,4R)-4,5-dihydroxyisoleucine
comments: In peptide sequencing work prior to 1968, this modification was reported
as a beta-methylleucine derivative that could arise by either beta-methylation
of leucine or gamma-methylation of isoleucine. The correct structure has been
determined to be derived from isoleucine without methylation.
synonyms:
- I
- (3R,4R)-4,5-dihydroxyisoleucine
- (2S,3R,4R)-2-amino-4,5-dihydroxy-3-methylpentanoic acid
- gamma,delta-dihydroxyisoleucine
- 4,5-dihydroxyisoleucine
- (2S,3R,4R)-2-amino-4,5-dihydroxy-3-methyl-pentanoic acid
- (2S,3R,4R)-2-amino-4,5-dihydroxy-3-methylpentanoic acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: ILX
- ns: mod
id: MOD:01378
- ns: resid
id: AA0449
- ns: pdb.ligand
id: ILX
structure: OC[C@@H]([C@@H]([C@@H](C(=O)O)[NH3+])C)O
base_monomers:
- I
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
- molecule: Monomer
element: H
position: 11
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
AA0579:
id: AA0579
name: (2S,3S)-3-hydroxyaspartic acid
comments: 'This diastereomeric form has been found in the ankyrin repeat domain
of many proteins. For the (2S,3R)-diastereomer, see RESID:AA0027. Generating
Enzyme: hypoxia-inducible factor-asparagine dioxygenase (EC 1.14.11.30).'
synonyms:
- D
- (2S,3S)-2-azanyl-3-oxidanyl-butanedioic acid
- (2S,3S)-2-amino-3-hydroxybutanedioic acid
- (3S)-3-hydroxy-L-aspartic acid
- (3s)-3-hydroxy-l-aspartic acid
- 2-amino-3-hydroxysuccinic acid
- L-threo-beta-hydroxyaspartic acid
- L-threo-3-hydroxyaspartic acid
- 3-hydroxyaspartic acid
- 2-azanyl-3-hydroxybutanedioic acid
identifiers:
- ns: mod
id: MOD:01919
- ns: chebi
id: CHEBI:10696
- ns: pdb-ccd
id: BHD
- ns: cas
id: 7298-99-9
- ns: pdb.ligand
id: BHD
- ns: resid
id: AA0579
structure: O=C[C@H]([C@@H](C(=O)[O-])O)[NH3+]
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
AA0431:
id: AA0431
name: 1'-(1,2,3-trihydroxyprop-2-yl)-L-histidine
synonyms:
- (S)-2-amino-3-[1-(1,2,3-trihydroxypropan-2-yl)-1H-imidazol-4-yl]propanoic acid
- H
- N(epsilon)-histidine dihydroxyacetone adduct
- 1-[1,2-dihydroxy-1-(hydroxymethyl)ethyl]-l-histidine
- N(tau)-(1,2,3-trihydroxypropan-2-yl)histidine
- tele-(1,2,3-trihydroxypropan-2-yl)histidine
- 1-[1,2-dihydroxy-1-(hydroxymethyl)ethyl]-L-histidine
- (2S)-2-amino-3-[1-(1,2,3-trihydroxypropan-2-yl)imidazol-4-yl]propanoic acid
identifiers:
- ns: pdb.ligand
id: HIQ
- ns: mod
id: MOD:00160
- ns: resid
id: AA0431
- ns: mod
id: MOD:01177
- ns: pdb-ccd
id: HIQ
structure: OCC(n1cnc(c1)C[C@@H](C(=O)O)[NH3+])(CO)O
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0343:
id: AA0343
name: N-carbamoyl-L-alanine
comments: Carbamoylation of the alpha-amino group can be artifactual, especially
when urea buffers are used.
synonyms:
- 2-ureidopropanoic acid
- N-carbamylalanine
- (S)-2-(carbamoylamino)propanoic acid
identifiers:
- ns: mod
id: MOD:00348
- ns: resid
id: AA0343
- ns: go
id: GO:0046945
structure: NC(=O)N[C@H](C(=O)O)C
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
AA0451:
id: AA0451
name: 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide
synonyms:
- 3-(oxidosulfanyl)-L-alanine
- C
- 6'-hydroxy-S-oxo-tryptathionine
- 2-((2R)-2-amino-2carboxyethyl)sulfinyl-3-((2S)-2-amino-2-carboxyethyl)-1H-indole
- s-oxy cysteine
identifiers:
- ns: mod
id: MOD:01380
- ns: resid
id: AA0451
- ns: pdb.ligand
id: CSX
- ns: pdb-ccd
id: CSX
structure: O=C[C@H](Cc1c([nH]c2c1ccc(c2)O)[S@](=O)C[C@@H](C(=O)O)N)[NH3+]
base_monomers:
- W
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 22
l_bond_atoms:
- molecule: Monomer
element: N
position: 25
r_displaced_atoms:
- molecule: Monomer
element: O
position: 24
- molecule: Monomer
element: H
position: 24
l_displaced_atoms:
- molecule: Monomer
element: H
position: 25
AA0493:
id: AA0493
name: N-(dihydroxymethyl)-L-methionine
comments: 'The formyl group of N-formylmethionine, as an aldehyde, may undergo
spontaneous addition of water to form a dihydoxymethyl group. It is detectable
by mass spectrometry and other methods. Although appropriate, the keyword "thioether
bond" normally does not appear for this amino acid. Generating Enzyme: methionine--tRNA
ligase (EC 6.1.1.10); methionyl-tRNA formyltransferase (EC 2.1.2.9).'
synonyms:
- N-formyl-L-methionine hydrate
- N-orthoformylmethionine
- (2S)-2-[(dihydroxymethyl)amino]-4-(methylsulfanyl)butanoic acid
identifiers:
- ns: mod
id: MOD:01446
- ns: resid
id: AA0493
- ns: mod
id: MOD:01447
- ns: pdb.ligand
id: CXM
structure: CSCC[C@@H](C(=O)O)NC(O)O
base_monomers:
- M
- AA0021
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
AA0362:
id: AA0362
name: O-sulfo-L-threonine
synonyms:
- threonine sulfate ester
- O3-sulfothreonine
- O3-sulfonothreonine
- 2-amino-3-hydroxybutanoic acid 3-sulfate
- (2S,3R)-2-amino-3-(sulfooxy)butanoic acid
identifiers:
- ns: resid
id: AA0362
- ns: mod
id: MOD:00367
- ns: go
id: GO:0050985
structure: OC(=O)[C@H]([C@H](OS(=O)(=O)[O-])C)[NH3+]
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
AA0112:
id: AA0112
name: 3-methyl-L-lanthionine
comments: "There are 3 chiral centers, so there are 8 possible stereoisomers.\
\ Bacterial peptidyl-cysteine dehydroalanine/dehydrobutyrine ligase and peptide\
\ conformation preferentially produce the (2S,3S,2'R) diastereomer. The cysteine\
\ maintains its L configuration (R chirality), while the threonine 2-aminobutanoate\
\ skeleton has a D configuration (S chirality). For the (2R,3R,2'R) diastereomer,\
\ see RESID:AA0610. Generating Enzyme: peptidyl-phosphoserine/phosphothreonine\
\ dehydratase (EC 4.2.1.-); peptidyl-cysteine dehydroalanine/dehydrobutyrine\
\ ligase (EC 6.2.-.-)."
synonyms:
- 3-methyl-D,L-lanthionine
- (2S,3S,6R)-2,6-diamino-3-methyl-4-thiaheptanedioic acid
- cysteine-3-D-butyrine thioether
- (2S,3S,2'R)-2-amino-3-[(2-amino-2-carboxyethyl)thio]butanoic acid
- (2S-[2R*,3R*(S*)])-2-amino-3-[(2-amino-2-carboxyethyl)thio]butanoic acid
- (2S,3S,6R)-3-methyllanthionine
- (2S,3S)-2-amino-3-([(2R)-2-amino-2-carboxyethyl]sulfanyl)butanoic acid
identifiers:
- ns: mod
id: MOD:00121
- ns: cas
id: 42849-28-5
- ns: pdb.ligand
id: DBB
- ns: go
id: GO:0018081
- ns: resid
id: AA0112
- ns: chebi
id: CHEBI:20118
structure: O=C[C@H](CS[C@H]([C@H](C(=O)O)[NH3+])C)[NH3+]
base_monomers:
- T
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
AA0214:
id: AA0214
name: L-citrulline
comments: 'Generating Enzyme: protein-arginine deiminase (EC 3.5.3.15).'
synonyms:
- N5-carbamylornithine
- N~5~-carbamoyl-L-ornithine
- alpha-amino-delta-ureidovaleric acid
- delta-ureidonorvaline
- N5-carbamoylornithine
- (2S)-5-(aminocarbonylamino)-2-azanyl-pentanoic acid
- R
- (S)-2-amino-5-(carbamoylamino)pentanoic acid
- citrulline
- 2-amino-5-(aminocarbonyl)aminopentanoic acid
- N5-(aminocarbonyl)ornithine
identifiers:
- ns: mod
id: MOD:00219
- ns: pdb.ligand
id: CIR
- ns: cas
id: 372-75-8
- ns: pdb-ccd
id: CIR
- ns: go
id: GO:0018101
- ns: resid
id: AA0214
structure: NC(=O)NCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
AA0185:
id: AA0185
name: L-3-oxoalanine
comments: 'The modified cysteine is found in sulfatases at the second position
in the sequence motif [L/V]C[A/C/S/T]PSR. In at least one case, the oxidation
acceptor or cofactor for the generating enzyme is known to be S-adenosylmethionine.
The generating enzyme activity acting on serine would be EC 1.1.99.-, and acting
on cysteine would be EC 1.8.99.-. This modification should not be confused with
N-formylglycine (see RESID:AA0057). The use of the misleading, non-standard
name "C-alpha-formyl glycine" should be avoided. This active site residue occurs
in the hydrated form, 2-amino-3,3-dihydroxypropanoic acid, as observed in crystallographic
structures. See RESID:AA0492. The PDB Hetgroup FGL was originally designated
as the "C(alpha)-formyl glycine" active site residue L-3-oxoalanine observed
in its hydrated form. That structure, a gem-diol with an sp(3) carbon, was misinterpreted
as a carboxyl with an sp(2) carbon, and assigned to aminomalonic acid (see RESID:AA0458)
instead. Generating Enzyme: sulfatase maturing enzyme (sulfatase modifying factor,
C-alpha-formylglycine-generating enzyme) (EC 1.1.99.-) #link SER; sulfatase
maturing enzyme (sulfatase modifying factor, C-alpha-formylglycine-generating
enzyme) (EC 1.8.99.-) #link CYS.'
synonyms:
- L-amino-malonic acid semialdehyde
- 2-amino-3-oxopropionic acid
- G
- 2-aminopropanedioic acid
- L-aminomalonaldehydic acid
- L-serinesemialdehyde [misnomer]
- (S)-2-amino-3-oxopropanoic acid
- aminopropanedioic acid
- C(alpha)-formylglycine [misnomer]
identifiers:
- ns: cas
id: 5735-66-0
- ns: go
id: GO:0018083
- ns: pdb.ligand
id: FGL
- ns: mod
id: MOD:00193
- ns: mod
id: MOD:00835
- ns: pdb-ccd
id: FGL
- ns: resid
id: AA0185
structure: O=CC(C(=O)O)N
base_monomers:
- S
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
AA0386:
id: AA0386
name: O-octanoyl-L-threonine
comments: 'Generating Enzyme: ghrelin O-acyltransferase, GOAT (EC 2.3.1.-).'
synonyms:
- L-threonine octanoate ester
- (2S)-2-amino-3-(octanoyloxy)butanoic acid
- O3-octanoyl-L-threonine
identifiers:
- ns: mod
id: MOD:00391
- ns: resid
id: AA0386
- ns: go
id: GO:0042050
structure: C[C@H]([C@H]([NH3+])C(=O)O)OC(=O)CCCCCCC
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
AA0181:
id: AA0181
name: dehydroalanine
comments: 'The modification of serine to dehydroalanine coupled with the formation
of 5-imidazolinone by the two neighboring residues produces the 4-methylidene-imidazole-5-one
(MIO) active site of some amino acid ammonia-lyases that differs by UV and mass
spectrometric evidence from other known dehydroalanine containing peptides not
containing the second modification. The formation of iodinated thyronine, O-(4-hydroxyphenyl)-tyrosine,
by phenoxy radical transfer from tyrosine in thyroglobulin produces dehydroalanine
as a by-product. See RESID:AA0177 and RESID:AA0178. The formation of S-(2-aminovinyl)-L-cysteine,
see RESID:AA0548, requires that an interior cysteine first undergoes oxidative
dethiolation to form dehydroalanine. This reaction is normally followed by formation
of an L-lanthionine through reformation of an L-cysteine in a thioether bond
with the C-terminal cysteine. The C-terminal cysteine is subsequently decarboxylated.
Because the intermediate dehydroalanine formed from cysteine is not normally
observed, it is not annotated as a feature in UniProt. Either free or in a peptide
chain, dehydroalanine is unstable, undergoing hydrolysis with formation of 2-hydroxyalanine
which can, like 2-hydroxyglycine (see RESID:AA0434), decompose by deamination
breaking the peptide backbone to form a peptide amide and a pyruvoyl peptide
(see RESID:AA0127). A 2,3-didehydro amino acid blocks Edman degradation. Generating
Enzyme: protein-cysteine dethiolase (EC 4.4.1.-) #link CYS; autocatalytic #link
SEC; protein-serine dehydratase (EC 4.2.1.-) #link SER.'
synonyms:
- 2,3-didehydroalanine
- 2-aminopropenoic acid
- anhydroserine
- 2-aminoacrylic acid
- 4-methylidene-imidazole-5-one (MIO) active site
- Dha
identifiers:
- ns: go
id: GO:0018250
- ns: pdb.ligand
id: DHA
- ns: resid
id: AA0181
- ns: chebi
id: CHEBI:17123
- ns: mod
id: MOD:00824
- ns: mod
id: MOD:00793
- ns: cas
id: 1948-56-7
- ns: mod
id: MOD:01954
- ns: mod
id: MOD:00189
structure: NC(=C)C(=O)O
base_monomers:
- U
- S
- Y
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0296:
id: AA0296
name: O-(N-acetylglucosamine-1-phosphoryl)-L-serine
comments: 'See also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291,
RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402, RESID:AA0404,
RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines. Generating
Enzyme: UDP-N-acetylglucosamine:serine-protein N-acetylglucosamine-1-phosphotransferase
(EC 2.7.8.-).'
synonyms:
- O3-(N-acetylglucosamine-1-phosphoryl)-L-serine
- O3-L-serine 2-(acetylamino)-2-deoxy-D-glucopyranose 1-phosphodiester
- O-beta(N-acetyl-glucosamine-alpha1-phosphate)serine
- (2S)-2-amino-3-[([(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)oxy][hydroxy]phosphoryl)oxy]propanoic
acid
identifiers:
- ns: mod
id: MOD:00301
- ns: go
id: GO:0018425
- ns: cas
id: 6866-69-9
- ns: resid
id: AA0296
structure: OC[C@H]1O[C@H](OP(=O)(OC[C@@H](C(=O)O)[NH3+])[O-])[C@@H]([C@H]([C@@H]1O)O)NC(=O)C
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
- molecule: Monomer
element: H
position: 17
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0581:
id: AA0581
name: L-methionine sulfoxide
comments: 'The S-oxide of methionine is a chiral center. The oxidized methionine
in actin has been determined to be the (R)-sulfoxide. The methionine (R)-sulfoxides
in actin can be reduced to methionine by methionine-R-sulfoxide reductase B1,
MsrB1 (EC 1.8.4.-). Generating Enzyme: protein-methionine sulfoxide oxidase
Mical1 (EC 1.14.13.-).'
synonyms:
- (2S)-2-amino-4-[(R)-methylsulfinyl]butanoic acid
- M
- methionine sulfoxide
- L-methionine (R)-S-oxide
identifiers:
- ns: mod
id: MOD:00721
- ns: pdb.ligand
id: SME
- ns: resid
id: AA0581
- ns: pdb-ccd
id: SME
- ns: cas
id: 3226-66-2
- ns: chebi
id: CHEBI:45764
structure: C[S@@](=O)CC[C@@H](C(=O)O)[NH3+]
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
AA0374:
id: AA0374
name: L-serine microcin E492 siderophore ester
synonyms:
- N-[5-(6-O-seryl-beta-glucosyl)-2,3-dihydroxybenzoyl]-O-[N-(2,3-dihydroxybenzoyl)-O-[N-(2,3-dihydroxybenzoyl)seryl]seryl]serine
identifiers:
- ns: mod
id: MOD:00379
- ns: resid
id: AA0374
- ns: go
id: GO:0051263
structure: OC[C@@H](C(=O)OC[C@@H](C(=O)OC[C@@H](C(=O)[O-])NC(=O)c1cc(cc(c1O)O)[C@@H]1O[C@H](COC(=O)[C@H](CO)N)[C@H]([C@@H]([C@H]1O)O)O)NC(=O)c1cccc(c1O)O)NC(=O)c1cccc(c1O)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
AA0252:
id: AA0252
name: dipyrrolylmethanemethyl-L-cysteine
comments: The pyrromethane cofactor is synthesized on the enzyme autocatalytically
by condensation of two porphobilinogen molecules.
synonyms:
- (2S)-3-[5-[4-(2-carboxy)ethyl-3-carboxymethyl-1-pyrrol-2-yl]methyl-4-(2-carboxy)ethyl-3-carboxymethyl-1-pyrrol-2-yl]methylthio-2-aminopropanoic
acid
- pyrromethane cofactor
- 3-[5-(3-acetic acid-4-propanoic acid-1-pyrrol-2-yl)methyl-3-acetic acid-4-propanoic
acid-1-pyrrol-2-yl]methylthio-2-aminopropanoic acid
- dipyrrolylmethyl-L-cysteine
- dipyrromethane cofactor
- dipyrrole cofactor
identifiers:
- ns: chebi
id: CHEBI:23842
- ns: mod
id: MOD:00257
- ns: resid
id: AA0252
- ns: cas
id: 29261-13-0
- ns: pdb.ligand
id: DPM
- ns: go
id: GO:0018160
structure: O=C[C@H](CSCc1[nH]c(c(c1CC(=O)[O-])CCC(=O)[O-])Cc1[nH]cc(c1CC(=O)[O-])CCC(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
AA0427:
id: AA0427
name: S-phycourobilin-L-cysteine
comments: There are additional chiral centers at C-3alpha, C-4, and C-16.
synonyms:
- phycourobilin cysteine adduct
- 18-ethenyl-3-[1-(2-amino-2-carboxyethylsulfanyl)ethyl]-2,3,15,16-dihydro-2,7,13,17-tetramethyl-1,19-dioxo-(21H,22H,24H)-bilin-8,12-dipropanoic
acid
- PUB
- (2S,3R,16R)-18-ethenyl-3-[(1R)-1-([(R)-2-amino-2-carboxyethyl]sulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-4,5,15,16-tetrahydrobiline-1,19(21H,22H,24H)-dione
identifiers:
- ns: mod
id: MOD:01175
- ns: cas
id: 61932-71-6
- ns: resid
id: AA0427
structure: O=C[C@H](CS[C@@H](C1=C(C)C(=O)N[C@H]1Cc1[nH]c(c(c1C)CCC(=O)[O-])Cc1[nH]c(c(c1CCC(=O)[O-])C)C[C@H]1NC(=O)C(=C1C)C=C)C)[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 27
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
r_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
AA0169:
id: AA0169
name: S-(ADP-ribosyl)-L-cysteine
comments: 'The anomeric form of the pertussis toxin product has not been characterized;
the alpha form is presented. The keywords "phosphoprotein" and "thioether bond"
are not used with toxin modification. Generating Enzyme: NAD(P)+--cysteine ADP-ribosyltransferase
(EC 2.4.2.-).'
synonyms:
- S-alpha-D-ribofuranosyl-L-cysteine 5'->5'-ester with adenosine 5'-(trihydrogen
diphosphate)
- (R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic
acid
- S-L-cysteine alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen
diphosphate)
identifiers:
- ns: go
id: GO:0006471
- ns: resid
id: AA0169
- ns: mod
id: MOD:00178
structure: OC(=O)[C@H](CS[C@@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)(OP(=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)[O-])[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 51
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 51
- molecule: Monomer
element: H
position: 51
charge: 1
AA0083:
id: AA0083
name: L-asparagine amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- (2S)-2-aminobutanediamide
- asparaginamide
identifiers:
- ns: mod
id: MOD:00092
- ns: go
id: GO:0018036
- ns: resid
id: AA0083
- ns: chebi
id: CHEBI:21243
- ns: cas
id: 16748-73-5
- ns: pdb.ligand
id: NH2
structure: NC(=O)C[C@@H](C(=O)N)[NH3+]
base_monomers:
- N
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
F, Y, Y:
id: AA0595
name: coelenterazine
comments: The structure of the amino acid components of coelenterazine suggest
that it is biosynthesized from a phenylalanyl-tyrosyl-tyrosine peptide. This
entry presents coelenterazine as a modification produced by the cross-linking
of a tripeptide precursor. For coelenterazine as a heterogen cross-linked to
a cysteine see RESID:AA0526.
synonyms:
- 8-benzyl-2-(4-hydroxybenzyl)-6-(4-hydroxyphenyl)imidazo[1,2-a]pyrazin-3(7H)-one
- Oplophorus luciferin
identifiers:
- ns: cas
id: 55779-48-1
- ns: mod
id: MOD:01949
- ns: chebi
id: CHEBI:2311
- ns: resid
id: AA0595
structure: Oc1ccc(cc1)Cc1nc2n(c1=O)cc([nH]c2Cc1ccccc1)c1ccc(cc1)O
base_monomers:
- F
- Y
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
AA0484:
id: AA0484
name: L-phenylalanine thiazoline-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue. Generating Enzyme: peptidyl-cysteine cyclase (EC 4.2.1.-).'
synonyms:
- (4R)-2-[(1S)-1-amino-2-phenylethyl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid
- 2-[1-azanyl-2-phenylethyl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid
identifiers:
- ns: resid
id: AA0484
- ns: mod
id: MOD:01407
structure: '[NH3+][C@H]([C@H]1SC[C@H](N1)C(=O)O)Cc1ccccc1'
base_monomers:
- F
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
- molecule: Monomer
element: H
position: 16
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
E, N:
id: AA0593
name: 2-(2-aminosuccinimidyl)pentanedioic acid
comments: 'This cross-link is formed by the condensation of an aspartic acid or
asparagine residue with the alpha-amido of the following residue. Generating
Enzyme: autocatalytic.'
synonyms:
- (4S)-4-[(3S)-3-amino-2,5-dioxopyrrolidin-1-yl]-5-oxopentanoic acid
- aspartimide glutamic acid
identifiers:
- ns: mod
id: MOD:01941
- ns: mod
id: MOD:01940
- ns: pdb.ligand
id: SNN
- ns: resid
id: AA0593
structure: O=C[C@@H](N1C(=O)C[C@@H](C1=O)N)CCC(=O)[O-]
base_monomers:
- N
- D
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
AA0529:
id: AA0529
name: N-(glycyl)-L-cysteine
comments: This modified carboxyl end glycine residue is produced by transamidation
of S-(glycyl)-L-cysteine (see RESID:AA0206) transiently forming a peptide bond
to a free cysteine before the cysteine is released by a peptidase activity.
synonyms:
- (2R)-2-[(aminoacetyl)amino]-3-sulfanylpropanoic acid
- N-(2-amino-1-oxoethyl)cysteine
identifiers:
- ns: mod
id: MOD:01778
- ns: resid
id: AA0529
structure: SC[C@@H](C(=O)[O-])NC(=O)C[NH3+]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
AA0557:
id: AA0557
name: L-cysteine sulfinyl phosphate
comments: This modification is probably produced as an intermediate during the
ATP mediated reduction of cysteine sulfinic acid (see RESID:AA0262) formed in
some proteins during oxidative stress.
synonyms:
- (2R)-2-amino-3-[(phosphonooxy)sulfinyl]propanoic acid
- cysteine sulfinic phosphoryl ester
identifiers:
- ns: resid
id: AA0557
- ns: mod
id: MOD:01847
structure: O[S@](OP(=O)(O)O)C[C@@H](C(=O)O)N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
AA0478:
id: AA0478
name: (2S,3S)-3-hydroxyasparagine
comments: 'This diastereomeric form has been found in the C-terminal transactivation
domain (CAD) of hypoxia-inducible factor (HIF), and in the ankyrin repeat domains
of notch 1, which probably also contains the other diastereomeric form of the
modification in its EGF domains. The PDB group code includes models with both
the (2S,3R) and the (2S,3S) stereoconfiguration. Generating Enzyme: hypoxia-inducible
factor-asparagine dioxygenase (EC 1.14.11.30).'
synonyms:
- (2S,3S)-2,4-diamino-3-hydroxy-4-oxobutanoic acid
- (2S,3S)-2-amino-3-hydroxy-4-butanediamic acid
- L-threo-beta-hydroxyasparagine
identifiers:
- ns: chebi
id: CHEBI:50789
- ns: mod
id: MOD:01401
- ns: resid
id: AA0478
- ns: pdb.ligand
id: AHB
structure: OC(=O)[C@H]([C@@H](C(=O)N)O)N
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
AA0619:
id: AA0619
name: N,N,N-trimethylglyine
comments: 'This modification is the major post-translational modification in the
methylation of N-terminal glycine. See also RESID:AA0063 and RESID:AA0620. Consult
FAQ at http://pir.georgetown.edu/resid/faq.shtml#q12 concerning calculation
of the difference formula. It is not clear whether "N-terminal methyltransferase"
defined in EC 2.1.1.244 is intended to exclude an enzyme activity that methylates
N-terminal glycine, or whether there are distinguishable enzyme activities.
Generating Enzyme: protein N-terminal methyltransferase (EC 2.1.1.244).'
synonyms:
- 2-trimethylammonioacetate
- carboxymethyl-trimethylazanium
- N,N,N-trimethylglycinium
- 1-carboxy-N,N,N-trimethylmethanazanium
- betaine
- carboxy-N,N,N-trimethylmethanaminium
- N,N,N-trimethylglycine cation
- (trimethylammonio)ethanoic acid
- glycine betaine
identifiers:
- ns: cas
id: 107-43-7
- ns: resid
id: AA0619
- ns: mod
id: MOD:01982
- ns: chebi
id: CHEBI:17750
structure: OC(=O)C[N](C)(C)C
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
AA0423:
id: AA0423
name: O-acetyl-L-threonine
comments: O-acetylation of threonine in host kinases is catalyzed by yersinia
toxin blocking the normal phosphorylation.
synonyms:
- O-acetylthreonine
- (2S,3R)-3-(acetyloxy)-2-aminobutanoic acid
- threonine acetate ester
identifiers:
- ns: resid
id: AA0423
- ns: mod
id: MOD:01171
- ns: cas
id: 17012-42-9
- ns: pdb.ligand
id: TH5
structure: CC(=O)O[C@@H]([C@@H](C(=O)O)[NH3+])C
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
- molecule: Monomer
element: H
position: 11
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
AA0401:
id: AA0401
name: O-galactosyl-L-threonine
comments: 'See also RESID:AA0155, RESID:AA0247, RESID:AA0399, RESID:AA0403, RESID:AA0405,
and RESID:AA0515 for other O-glycosylated threonines. Generating Enzyme: galactosyltransferase
(EC 2.4.1.-).'
synonyms:
- O-glycosylthreonine
- O3-galactosylthreonine
- (2S,3R)-2-amino-3-(alpha-D-galactopyranosyloxy)butanoic acid
identifiers:
- ns: mod
id: MOD:00809
- ns: resid
id: AA0401
structure: OC[C@H]1O[C@H](O[C@@H]([C@@H](C(=O)O)[NH3+])C)[C@@H]([C@H]([C@H]1O)O)O
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0341:
id: AA0341
name: 2-(S-L-cysteinyl)-D-phenylalanine
comments: The D-stereoisomer of the 2-S-cysteinyl substituted phenylalanine has
S configuration.
synonyms:
- (2S,5R)-2,5-diamino-3-thia-2-phenylmethylhexanedioic acid
- (2S)-2-amino-2-[(2R)-2-amino-2-carboxyethyl]sulfanyl-3-phenylpropanoic acid
- alpha-(L-cystein-S-yl)-D-phenylalanine
identifiers:
- ns: go
id: GO:0046925
- ns: resid
id: AA0341
- ns: mod
id: MOD:00346
structure: O=C[C@](Cc1ccccc1)(SC[C@@H](C(=O)O)[NH3+])N
base_monomers:
- F
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
- molecule: Monomer
element: H
position: 17
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0442:
id: AA0442
name: (2S)-4-hydroxyleucine
synonyms:
- (2S)-2-amino-4-hydroxy-4-methylpentanoic acid
- gamma-hydroxyleucine
identifiers:
- ns: mod
id: MOD:01372
- ns: resid
id: AA0442
structure: OC(=O)[C@H](CC(O)(C)C)[NH3+]
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
AA0546:
id: AA0546
name: L-allo-isoleucine
comments: 'Generating Enzyme: protein-isoleucine 3-epimerase (EC 5.1.1.-).'
synonyms:
- 2-azanyl-3-methylpentanoic acid
- alpha-amino-beta-methylvaleric acid
- allo-L-isoleucine
- 3-methyl-norvaline
- (2S,3R)-2-amino-3-methylpentanoic acid
- L-threo-isoleucine
identifiers:
- ns: chebi
id: CHEBI:30008
- ns: cas
id: 1509-34-8
- ns: mod
id: MOD:01840
- ns: resid
id: AA0546
structure: CC[C@H]([C@@H](C(=O)O)[NH3+])C
base_monomers:
- I
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
AA0103:
id: AA0103
name: S-12-hydroxyfarnesyl-L-cysteine
comments: Formation of S-12-hydroxyfarnesylcysteine may be coupled with subsequent
cleavage of a carboxy-terminal tripeptide for the CAAX motif and methyl esterification
of the farnesylated cysteine. See L-cysteine methyl ester (RESID:AA0105).
synonyms:
- (2R)-2-amino-3-([(2E,6E,10Z)-12-hydroxy-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]sulfanyl)propanoic
acid
- 2-amino-3-(12-hydroxy-3,7,11-trimethyl-3,6,10-dodecatrienylthio)propanoic acid
identifiers:
- ns: mod
id: MOD:00112
- ns: go
id: GO:0018227
- ns: resid
id: AA0103
structure: OC/C(=C\CC/C(=C/CC/C(=C/CSC[C@@H](C(=O)O)[NH3+])/C)/C)/C
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
- molecule: Monomer
element: H
position: 20
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
AA0087:
id: AA0087
name: L-glutamic acid 1-amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- 4,5-diamino-5-oxopentanoic acid
- isoglutamine
- 4-amido-4-carbamoyl-butyric acid
- E
- L-alpha-glutamine
- (4S)-4,5-diamino-5-oxo-pentanoic acid
- (2S)-2-amino-1-pentanediamic acid
identifiers:
- ns: resid
id: AA0087
- ns: go
id: GO:0018040
- ns: chebi
id: CHEBI:21305
- ns: cas
id: 328-48-3
- ns: mod
id: MOD:00096
- ns: pdb-ccd
id: GMA
- ns: pdb.ligand
id: NH2
structure: '[O-]C(=O)CC[C@@H](C(=O)N)[NH3+]'
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
AA0432:
id: AA0432
name: S-(aspart-4-yloxy) thiocarbonate
comments: This modification was originally observed in the enzyme expressed in
Escherichia coli. It was not chemically confirmed or characterized. It did not
appear in a later model at higher resolution by the same group.
synonyms:
- D
- (2S)-2-amino-4-(carboxysulfanyl)oxy-4-oxobutanoic acid
- o-(carboxysulfanyl)-4-oxo-l-homoserine
- O-(carboxysulfanyl)-4-oxo-D-homoserine
- (2R)-2-amino-4-carboxysulfanyloxy-4-oxo-butanoic acid
- 4-aspartyloxysulfanylcarbonate
- O-carboxysulfanyl-4-oxo-L-homoserine
identifiers:
- ns: pdb.ligand
id: OHS
- ns: resid
id: AA0432
- ns: pdb-ccd
id: OHS
- ns: mod
id: MOD:01178
structure: O=C(C[C@@H](C(=O)O)[NH3+])OSC(=O)[O-]
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
- molecule: Monomer
element: H
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
AA0550:
id: AA0550
name: 2-(3-methylbutanoyl)-5-hydroxy-oxazole-4-carbothionic acid
comments: The amino group of the following amino acid forms a thiopeptide bond.
The amino(sulfanyl)methylidene tautomeric form is shown in the diagram and model.
The biosynthesis of this modification from the encoded cysteine peptide has
not been elaborated.
synonyms:
- (4Z)-4-[hydroxy(sulfanyl)methylidene]-2-(3-methylbutanoyl)-1,3-oxazol-5(4H)-one
[tautomer]
- 5-hydroxy-2-(3-methylbutanoyl)-1,3-oxazole-4-carbothioic O-acid
identifiers:
- ns: resid
id: AA0550
- ns: mod
id: MOD:01844
- ns: pdb.ligand
id: 8LI
structure: '[S-]/C=C/1\N=C(OC1=O)C(=O)CC(C)C'
base_monomers:
- L
- C
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
AA0444:
id: AA0444
name: (2S,4R)-5-oxoleucine
comments: The oxidation artifacts 5-hydroxyleucine and 5-oxoleucine can form autocatalytically
and stereospecifically, but not selectively. It is not clear whether the modified
residue subsequently takes part in catalytic reactions at the active site of
alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 (ABH3).
synonyms:
- (4R)-5-oxo-L-leucine
- (2S,4R)-2-amino-4-methyl-5-oxo-pentanoic acid
- (4r)-5-oxo-l-leucine
- L
- (2S,4R)-2-amino-4-methyl-5-oxopentanoic acid
identifiers:
- ns: pdb-ccd
id: LED
- ns: mod
id: MOD:01374
- ns: resid
id: AA0444
- ns: chebi
id: CHEBI:43739
- ns: pdb.ligand
id: LED
structure: O=C[C@@H](C[C@@H](C(=O)O)[NH3+])C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
AA0614:
id: AA0614
name: 5-glutamyl coenzyme A thioester
comments: 'Generating Enzyme: autocatalytic.'
synonyms:
- 5-glutamyl 4-[(3'-phospho-adenosyl-5'-diphosphoryl)oxy]pantetheine thioester
- (2S)-2-amino-5-([2-(3-[(2R)-2-hydroxy-3,3-dimethyl-4-([3'-phospho-adenosyl-5'-diphosphoryl]-oxy)-butanamido]-propanamido)-ethyl]-sulfanyl)-5-oxopentanoic
acid
- (2S)-2-amino-5-(2-[([3-([(2R)-2-hydroxy-3,3-dimethyl-4-([3'-phospho-adenosyl-5'-diphosphoryl]-oxy)-butanoyl]-amino)-propanoyl]-amino)-ethyl]-sulfanyl)-5-oxopentanoic
acid
identifiers:
- ns: mod
id: MOD:01972
- ns: resid
id: AA0614
structure: O=C(NCCSC(=O)CC[C@@H](C(=O)O)[NH3+])CCNC(=O)[C@@H](C(COP(=O)(OP(=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1OP(=O)([O-])[O-])O)n1cnc2c1ncnc2N)[O-])[O-])(C)C)O
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0200:
id: AA0200
name: D-valine
comments: 'Generating Enzyme: protein-valine epimerase (EC 5.1.1.-).'
synonyms:
- (R)-2-amino-3-methylbutanoic acid
- alpha-aminoisovaleric acid
- alpha-amino-beta-methylbutyric acid
identifiers:
- ns: resid
id: AA0200
- ns: cas
id: 640-68-6
- ns: pdb.ligand
id: DVA
- ns: mod
id: MOD:00705
- ns: chebi
id: CHEBI:30016
structure: '[NH3+][C@@H](C(=O)O)C(C)C'
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AA0056:
id: AA0056
name: S-acetyl-L-cysteine
synonyms:
- (2R)-2-amino-3-ethanoylsulfanyl-propanoic acid
- cysteine acetate thioester
- C
- S-acetyl-L-cysteine
- (2R)-3-acetylsulfanyl-2-aminopropanoic acid
- s-acetyl-cysteine
- S-acetylcysteine
- 2-azanyl-3-(acetylsulfanyl)propanoic acid
- 2-amino-3-(acetylthio)propanoic acid
identifiers:
- ns: go
id: GO:0018219
- ns: cas
id: 15312-11-5
- ns: pdb.ligand
id: SCY
- ns: mod
id: MOD:00065
- ns: pdb-ccd
id: SCY
- ns: resid
id: AA0056
structure: CC(=O)SC[C@@H](C(=O)O)N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
AA0435:
id: AA0435
name: L-aspartic acid 4-methyl ester
comments: An enzyme acting to form the methyl ester of L-aspartyl peptides might
interfere with the D-aspartyl peptide repair mechanism.
synonyms:
- 4-methyl L-aspartate
- 2-aminobutanedioic acid 4-methyl ester
- 4-methyl L-2-aminosuccinic acid
- (2S)-2-amino-4-methoxy-4-oxobutanoic acid
- 4-methyl L-hydrogen aspartate
- aspartic acid beta-methyl ester
- aspartic acid 4-methyl ester
identifiers:
- ns: mod
id: MOD:01181
- ns: cas
id: 16856-13-6
- ns: resid
id: AA0435
structure: COC(=O)C[C@H]([NH3+])C(=O)O
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
AA0102:
id: AA0102
name: S-farnesyl-L-cysteine
comments: 'Formation of S-farnesycysteine may be coupled with subsequent cleavage
of a carboxy-terminal tripeptide for the CXXX motif and methyl esterification
of the farnesylated cysteine. See L-cysteine methyl ester (RESID:AA0105). This
modification may be found at the first position in the sequence motif CXX[SAQCMT]*
where the second and third positions are usually aliphatic. Generating Enzyme:
protein-cysteine farnesyltransferase (EC 2.5.1.-).'
synonyms:
- 2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid
- (2R)-2-amino-3-([(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]sulfanyl)propanoic
acid
identifiers:
- ns: pdb.ligand
id: FAR
- ns: cas
id: 68000-92-0
- ns: go
id: GO:0018226
- ns: resid
id: AA0102
- ns: mod
id: MOD:00111
structure: C/C(=C\CSC[C@@H](C(=O)O)[NH3+])/CC/C=C(/CCC=C(C)C)\C
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
- molecule: Monomer
element: H
position: 11
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
AA0032:
id: AA0032
name: L-gamma-carboxyglutamic acid
comments: 'The gamma-carboxylation of glutamic acid residues is performed by a
vitamin K-dependent enzyme. Generating Enzyme: gamma-glutamyl carboxylase (EC
4.1.1.-).'
synonyms:
- 4-carboxyglutamic acid
- gamma-carboxy-glutamic acid
- (3S)-3-aminopropane-1,1,3-tricarboxylic acid
- E
- 3-azanylpropane-1,1,3-tricarboxylic acid
- (3S)-3-azanylpropane-1,1,3-tricarboxylic acid
- 3-amino-1,1,3-propanetricarboxylic acid
- 1-carboxyglutamic acid [misnomer]
identifiers:
- ns: mod
id: MOD:00041
- ns: pdb.ligand
id: CGU
- ns: cas
id: 53861-57-7
- ns: go
id: GO:0017187
- ns: chebi
id: CHEBI:61939
- ns: pdb-ccd
id: CGU
- ns: resid
id: AA0032
structure: O=C[C@H](CC(C(=O)[O-])C(=O)[O-])[NH3+]
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
AA0175:
id: AA0175
name: L-3'-bromophenylalanine
synonyms:
- meta-bromophenylalanine
- m-bromophenylalanine
- (S)-2-amino-3-(3-bromophenyl)propanoic acid
identifiers:
- ns: resid
id: AA0175
- ns: mod
id: MOD:00184
- ns: cas
id: 82311-69-1
- ns: go
id: GO:0018075
structure: OC(=O)[C@H](Cc1cccc(c1)Br)[NH3+]
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
AA0240:
id: AA0240
name: glycine oxazole-4-carboxylic acid
comments: 'Formed by the condensation of a serine hydroxyl with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-serine
cyclase (EC 4.2.1.-); peptidyl-oxazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-aminomethyl-1,3-oxazole-4-carboxylic acid
- 2-azanylmethyl-1,3-oxazole-4-carboxylic acid
identifiers:
- ns: resid
id: AA0240
- ns: mod
id: MOD:00245
- ns: go
id: GO:0018134
structure: NCc1occ(n1)C(=O)O
base_monomers:
- S
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
AA0263:
id: AA0263
name: L-3',4',5'-trihydroxyphenylalanine
synonyms:
- L-3,4,5-TOPA
- (S)-2-amino-3-(3,4,5-trihydroxyphenyl)propanoic acid
identifiers:
- ns: go
id: GO:0018172
- ns: mod
id: MOD:00268
- ns: resid
id: AA0263
structure: OC(=O)[C@H](Cc1cc(O)c(c(c1)O)O)[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0609:
id: AA0609
name: omega-N-(N-acetylamino)glucosyl-L-arginine
comments: 'This modification is produced in host proteins by a secretion system
effector of some enteropathogenic bacteria. The anomeric form of the product
has not been characterized; the beta form is presented. Generating Enzyme: [protein]-L-arginine
N-acetyl-D-glucosaminyl-transferase NleB (EC 2.4.1.-).'
synonyms:
- N(omega)-(2-acetamido-2-deoxy-D-glucopyranosyl)-L-arginine
- N(omega)-(2-N-acetylaminoglucosyl)arginine
- omega-N-(2-acetylamino-2-deoxy-D-glucopyranosyl)-L-arginine
- (2S)-2-amino-5-[(amino[(2-N-acetylamino-2-deoxy-D-glucopyranosyl)amino]methylidene)amino]pentanoic
acid
- NG-(2-acetamido-2-deoxy-D-glucopyranosyl)-L-arginine
- N(omega)-(2-acetylamino-2-deoxy-D-glucopyranosyl)-L-arginine
- omega-N-(2-N-acetylaminoglucosyl)arginine
- NG-(2-acetylamino-2-deoxy-D-glucopyranosyl)-L-arginine
- omega-N-(2-acetamido-2-deoxy-D-glucopyranosyl)-L-arginine
- NG-(2-N-acetylaminoglucosyl)arginine
identifiers:
- ns: mod
id: MOD:01967
- ns: resid
id: AA0609
structure: OC[C@H]1O[C@@H](N/C(=[NH+]\CCC[C@@H](C(=O)O)[NH3+])/N)[C@@H]([C@H]([C@@H]1O)O)NC(=O)C
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
- molecule: Monomer
element: H
position: 19
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
AA0428:
id: AA0428
name: S-15,16-dihydrobiliverdin-L-cysteine
comments: 15,16-dihydrobiliverdin transmits violet.
synonyms:
- 3'-cysteinyl-15,16-dihydrobiliverdin
- 15,16-dihydrobiliverdin cysteine adduct
- 3alpha-cysteinyl-15,16-dihydrobiliverdin
- (16R)-18-ethenyl-8,12-bis(2-carboxyethyl)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-2,7,13,17-tetramethyl-15,16-dihydrobilin-1,19(21H,24H)-dione
- DBV
- 15,16-dihydrobiliverdin IXalpha
- 18-ethenyl-8,12-bis(2-carboxyethyl)-3-(2-(cysteinyl-S)-ethyl)-2,7,13,17-tetramethylbiladiene-ab-1,19(16H,21H)-dione
- 15,16-Dhbv
identifiers:
- ns: resid
id: AA0428
- ns: pdb.ligand
id: DBV
- ns: mod
id: MOD:01142
- ns: cas
id: 137429-14-2
structure: O=C[C@H](CS[C@H](C1=C(C)C(=O)N/C/1=C\c1[nH]c(c(c1C)CCC(=O)[O-])Cc1[nH]c(c(c1CCC(=O)[O-])C)C[C@H]1NC(=O)C(=C1C)C=C)C)[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 26
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
r_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
AA0149:
id: AA0149
name: 4'-(L-tryptophan)-L-tryptophyl quinone
comments: 'Generating Enzyme: methylamine dehydrogenase activase MauG (EC 6.-.-.-).'
synonyms:
- TTQ
- 3-[(2S)-2-amino-2-carboxyethyl]-4-(3-[(2S)-2-amino-2-carboxyethyl]-1H-indol-2-yl)-6,7-indolinedione
- 2-amino-3-[2-[2-amino-3-(2-carboxyethyl)-6,7-dioxo-1H-indol-4-yl]-1H-indol-3-yl]propanoic
acid
- 4'-tryptophan-tryptophylquinone
- 4-(2'-tryptophyl)tryptophan-6,7-dione
- alpha,alpha'-diamino-6',7'-dihydro-6',7'-dioxo-(2,4'-bi-1H-indole)-3,3'-dipropanoic
acid
identifiers:
- ns: cas
id: 134645-25-3
- ns: resid
id: AA0149
- ns: mod
id: MOD:00158
- ns: chebi
id: CHEBI:20251
- ns: go
id: GO:0018069
structure: O=C[C@H](Cc1c[nH]c2c1C(=CC(=O)C2=O)c1[nH]c2c(c1C[C@@H](C(=O)O)[NH3+])cccc2)[NH3+]
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 27
l_bond_atoms:
- molecule: Monomer
element: N
position: 30
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 29
- molecule: Monomer
element: H
position: 29
l_displaced_atoms:
- molecule: Monomer
element: H
position: 30
- molecule: Monomer
element: H
position: 30
charge: 1
AA0545:
id: AA0545
name: N6-succinyl-L-lysine
comments: The responsible generating enzyme activity is not identified. This modification
can be reversed by Sirt5.
synonyms:
- 4-[[(5S)-5-amino-6-hydroxy-6-oxohexyl]amino]-4-oxobutanoate
- N(epsilon)-(succinyl)lysine
- 2-azanyl-6-[(3-carboxypropanoyl)azanyl]hexanoic acid
- succinyllysine
- (2S)-2-amino-6-[(3-carboxypropanoyl)amino]hexanoic acid
identifiers:
- ns: mod
id: MOD:01819
- ns: resid
id: AA0545
structure: O=C[C@H](CCCCNC(=O)CCC(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
AA0578:
id: AA0578
name: (2S,5S)-5-hydroxylysine
comments: 'This diastereomeric form has been found in some splicing regulatory
proteins. For the (2S,5R)-diastereomer, see RESID:AA0028. The Enzyme Commission
has not yet distinguished the different stereospecific enzyme activities. Generating
Enzyme: peptide-lysine 5-dioxygenase JMJD6 (EC 1.14.11.-).'
synonyms:
- 2,6-diamino-2,3,4,6-tetradeoxyhexonic acid
- alpha,epsilon-diamino-delta-hydroxycaproic acid
- 2,6-bisazanyl-5-hydroxyhexanoic acid
- L-threo-delta-hydroxylysine
- (2S,5S)-2,6-diamino-5-hydroxyhexanoic acid
- L-allo-delta-hydroxylysine
identifiers:
- ns: mod
id: MOD:01918
- ns: cas
id: 18899-29-1
- ns: resid
id: AA0578
structure: '[NH3+]C[C@H](CC[C@@H](C(=O)O)[NH3+])O'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0167:
id: AA0167
name: O-(phosphoribosyl dephospho-coenzyme A)-L-serine
comments: 'Generating Enzyme: holo-ACP synthase (EC 2.7.7.61).'
synonyms:
- O3-(phosphate-5-ribosyl-alpha-2-adenosine-5-diphosphate pantetheine)-L-serine
- O3-2'-(5''-phosphoribosyl-3'-dephosphocoenzyme A)-L-serine
- O3-(phosphoribosyl dephospho-coenzyme A)-L-serine
identifiers:
- ns: mod
id: MOD:00176
- ns: go
id: GO:0018247
- ns: resid
id: AA0167
structure: SCCNC(=O)CCNC(=O)[C@@H](C(COP(=O)(OP(=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O[C@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)(OC[C@@H](C(=O)O)[NH3+])[O-])n1cnc2c1ncnc2N)[O-])[O-])(C)C)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 54
l_bond_atoms:
- molecule: Monomer
element: N
position: 57
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 56
- molecule: Monomer
element: H
position: 56
l_displaced_atoms:
- molecule: Monomer
element: H
position: 57
- molecule: Monomer
element: H
position: 57
charge: 1
S, S:
id: AA0574
name: L-serine oxazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-serine
cyclase (EC 4.2.1.-); peptidyl-oxazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-[(1S)-1-amino-2-hydroxyethyl]-1,3-oxazole-4-carboxylic acid
- 2-[(1S)-1-azanyl-2-hydroxyethyl]-1,3-oxazole-4-carboxylic acid
identifiers:
- ns: mod
id: MOD:01903
- ns: resid
id: AA0574
structure: OC[C@@H](c1occ(n1)C(=O)O)N
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
AA0197:
id: AA0197
name: D-leucine
comments: 'Generating Enzyme: protein-leucine epimerase (EC 5.1.1.-).'
synonyms:
- (2R)-2-amino-4-methylpentanoic acid
- alpha-aminoisocaproic acid
identifiers:
- ns: mod
id: MOD:00204
- ns: cas
id: 328-38-1
- ns: go
id: GO:0019129
- ns: chebi
id: CHEBI:30005
- ns: resid
id: AA0197
- ns: pdb.ligand
id: DLE
structure: '[NH3+][C@@H](C(=O)O)CC(C)C'
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AA0514:
id: AA0514
name: O-(6'-phosphomannosyl)-L-threonine
comments: 'The alpha anomeric form is shown. See also RESID:AA0155, RESID:AA0247,
RESID:AA0399, RESID:AA0401, RESID:AA0403, and RESID:AA0405 for other O-glycosylated
threonines. Generating Enzyme: protein O-mannosyl transferase (EC 2.4.1.109);
protein O-mannose beta-1,4-N-acetylglucosaminyltransferase (EC 2.4.1.-); protein
O-(N-acetylglucosaminyl-beta-1,4)-mannose beta-1,4-N-acetylgalactosaminyltransferase
(EC 2.4.1.-); protein O-mannose 6-phosphotransferase (EC 2.7.1.-).'
synonyms:
- (2S,3R)-2-amino-3-[6-phosphonooxy-alpha-D-mannopyranosyloxy]butanoic acid
- O3-(6-phosphomannosyl)threonine
identifiers:
- ns: resid
id: AA0514
- ns: mod
id: MOD:01617
structure: '[NH3+][C@@H]([C@H](O[C@H]1O[C@H](COP(=O)([O-])[O-])[C@H]([C@H]([C@@H]1O)O)O)C)C(=O)O'
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 31
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 33
- molecule: Monomer
element: H
position: 33
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AA0194:
id: AA0194
name: D-phenylalanine
comments: 'Generating Enzyme: protein-phenylalanine epimerase (EC 5.1.1.-).'
synonyms:
- (R)-2-amino-3-phenylpropanoic acid
identifiers:
- ns: pdb.ligand
id: DPN
- ns: cas
id: 673-06-3
- ns: mod
id: MOD:00201
- ns: chebi
id: CHEBI:29996
- ns: resid
id: AA0194
- ns: go
id: GO:0019125
structure: '[NH3+][C@@H](C(=O)O)Cc1ccccc1'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AA0533:
id: AA0533
name: N-methyl-L-serine
comments: 'Polypeptides with monomethylated amino terminals can undergo premature
cleavage during the coupling step of an Edman degradation. This can result in
"preview" with both a residue and the following residue being seen from the
first step on through a sequence. Generating Enzyme: N-terminal RCC1 methyltransferase
(EC 2.1.1.-).'
synonyms:
- N-methylserine
- (2S)-3-hydroxy-2-(methylamino)propanoic acid
identifiers:
- ns: cas
id: 2480-26-4
- ns: go
id: GO:0035570
- ns: resid
id: AA0533
- ns: mod
id: MOD:01782
structure: C[NH2+][C@H](C(=O)O)CO
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
AA0068:
id: AA0068
name: omega-N,omega-N-dimethyl-L-arginine
comments: "This modification should not be confused with omega-N,omega-N'-dimethyl-L-arginine\
\ (see RESID:AA0067) or N2,N2-dimethyl-L-arginine (see RESID:AA0569). Generating\
\ Enzyme: histone-arginine N-methyltransferase (EC 2.1.1.125)."
synonyms:
- ng,ng-dimethyl-l-arginine
- N5-[(dimethylamino)(imino)methyl]ornithine
- asymmetric dimethylarginine
- (2S)-2-azanyl-5-[(N,N-dimethylcarbamimidoyl)amino]pentanoic acid
- NG,NG-dimethylarginine
- N~5~-(N,N-dimethylcarbamimidoyl)-L-ornithine
- R
- (2S)-2-amino-5-([(dimethylamino)(imino)methyl]amino)pentanoic acid
identifiers:
- ns: mod
id: MOD:00077
- ns: pdb.ligand
id: DA2
- ns: cas
id: 30315-93-6
- ns: resid
id: AA0068
- ns: go
id: GO:0018216
- ns: chebi
id: CHEBI:61896
- ns: pdb-ccd
id: DA2
structure: OC(=O)[C@H](CCCNC(=[NH2])N(C)C)[NH3+]
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
AA0202:
id: AA0202
name: L-isoglutamyl-polyglutamic acid
comments: This entry is for L-isoglutamyl-polyglutamic acid where there are 2
to 6 alpha-peptide linked glutamic acid residues attached to a peptide glutamyl
residue by an isopeptide bond. For a single glutamic acid attached to a peptide
glutamyl residue by an isopeptide bond, see 5-glutamyl glutamic acid, RESID:AA0612.
synonyms:
- gamma-glutamylpolyglutamic acid
identifiers:
- ns: go
id: GO:0018095
- ns: mod
id: MOD:00207
- ns: resid
id: AA0202
structure: O=C[C@H](CCC(=O)N[C@H](C(=O)[O-])CCC(=O)[O-])[NH3+]
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
AA0350:
id: AA0350
name: O3-(riboflavin phosphoryl)-L-serine
comments: This modification is predicted for proteins homologous to Na(+)-translocating
NADH:quinone oxidoreductase B and C chains in certain organisms where the position
corresponding to O3-(ribofavin phosphoryl)-threonine instead encodes serine.
synonyms:
- O3-seryl flavin mononucleotide
- (R)-2-amino-3-(riboflavin 5'-hydrogen phosphonoxy)propanoic acid
- O3-seryl FMN
identifiers:
- ns: resid
id: AA0350
- ns: go
id: GO:0050741
- ns: mod
id: MOD:00355
structure: O=c1[nH]c(=O)c2c([nH]1)n(C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(OC[C@@H](C(=O)O)[NH3+])[O-])O)O)O)c1=C[C@H](C(=Cc1n2)C)C
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 27
l_bond_atoms:
- molecule: Monomer
element: N
position: 30
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 29
- molecule: Monomer
element: H
position: 29
l_displaced_atoms:
- molecule: Monomer
element: H
position: 30
- molecule: Monomer
element: H
position: 30
charge: 1
AA0539:
id: AA0539
name: N-formyl-L-glutamic acid
synonyms:
- 2-formylaminopentanedioic acid
- 2-formamidopentanedioic acid
- (2S)-2-(formylamino)pentanedioic acid
- 2-(formylazanyl)pentanedioic acid
identifiers:
- ns: mod
id: MOD:01807
- ns: resid
id: AA0539
structure: O=CN[C@@H](CCC(=O)[O-])C=O
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 3
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 3
AA0297:
id: AA0297
name: O-(phosphoglycosyl-D-mannose-1-phosphoryl)-L-serine
comments: 'Mannose oligosaccharides and short phosphoglycan chains may be attached
to the mannose 1-phosphate at the 2 position. See also RESID:AA0154, RESID:AA0208,
RESID:AA0209, RESID:AA0210, RESID:AA0291, RESID:AA0296, RESID:AA0397, RESID:AA0398,
RESID:AA0400, RESID:AA0402, RESID:AA0404, RESID:AA0406, and RESID:AA0422 for
other O-glycosylated serines. Generating Enzyme: GDP-mannose:serine-protein
mannose-1-phosphotransferase (EC 2.7.8.-).'
synonyms:
- O-(alpha-D-mannosyl-1-phosphoryl)-L-serine
- O3-L-serine alpha-D-mannopyranose 1-phosphodiester
- O-[alpha-D-mannopyranosyloxy(hydroxy)phosphoryl]-L-serine
- O3-(D-mannose-1-phosphoryl)-L-serine
identifiers:
- ns: resid
id: AA0297
- ns: go
id: GO:0018426
- ns: mod
id: MOD:00302
structure: OC[C@H]1O[C@H](OP(=O)(OC[C@@H](C(=O)O)[NH3+])[O-])[C@H]([C@H]([C@@H]1O)O)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
- molecule: Monomer
element: H
position: 17
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0215:
id: AA0215
name: 4-hydroxy-L-arginine
comments: The stereochemistry for the second chiral center has not been resolved.
The (2S,4R) diastereomer is shown.
synonyms:
- c-gamma-hydroxy arginine
- gamma-hydroxyarginine
- 2-amino-5-[(aminoiminomethyl)amino]-4-hydroxypentanoic acid [tautomer]
- 2-amino-5-(carbamimidamido)-4-hydroxypentanoic acid [tautomer]
- 2-amino-5-guanidino-4-hydroxypentanoic acid
- amino{[(2R,4S)-4-amino-2,5-dihydroxy-5-oxopentyl]amino}methaniminium
- (2S,4Xi)-2-amino-5-[(diaminomethylidene)amino]-4-hydroxypentanoic acid
- C(gamma)-hydroxyarginine
- '[amino-[[(2R,4S)-4-amino-2,5-dihydroxy-5-oxo-pentyl]amino]methylidene]azanium'
- R
identifiers:
- ns: mod
id: MOD:00220
- ns: cas
id: 2524-31-4
- ns: pdb.ligand
id: ARO
- ns: pdb-ccd
id: ARO
- ns: resid
id: AA0215
- ns: go
id: GO:0018102
structure: O[C@H](C[C@@H](C(=O)O)[NH3+])C[NH+]=C(N)N
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
AA0287:
id: AA0287
name: N6-pyruvic acid 2-iminyl-L-lysine
synonyms:
- (2s)-2-amino-6-[(1-hydroxy-1-oxo-propan-2-ylidene)amino]hexanoic acid
- (E)-N~6~-(1-carboxyethylidene)-L-lysine
- (2S)-2-amino-6-([1-carboxyethylidene]amino)hexanoic acid
- K
- (2S)-2-azanyl-6-[(E)-(1-oxidanyl-1-oxidanylidene-propan-2-ylidene)amino]hexanoic
acid
identifiers:
- ns: pdb-ccd
id: KPI
- ns: mod
id: MOD:00292
- ns: go
id: GO:0018308
- ns: resid
id: AA0287
- ns: pdb.ligand
id: KPI
structure: O=C[C@H](CCCC[NH2+][C@@H](C(=O)[O-])C)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
AA0220:
id: AA0220
name: S-(6-FMN)-L-cysteine
comments: 'The keyword "phosphoprotein" is not used with flavin modifications
linked through the flavin. Generating Enzyme: autocatalytic.'
synonyms:
- (R)-2-amino-3-[6-riboflavin 5'-dihydrogen phosphate]sulfanylpropanoic acid
- 6-[S-cysteinyl]FMN
- 6-[S-cysteinyl]flavin mononucleotide
identifiers:
- ns: resid
id: AA0220
- ns: mod
id: MOD:00225
- ns: go
id: GO:0018310
- ns: pdb.ligand
id: FMN
structure: O=C1NC(=O)[C@@H]2C(=N1)N(C[C@@H]([C@@H]([C@@H](COP(=O)([O-])[O-])O)O)O)c1c(N2)c(SC[C@@H](C(=O)O)[NH3+])c(c(c1)C)C
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 35
l_bond_atoms:
- molecule: Monomer
element: N
position: 38
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 37
- molecule: Monomer
element: H
position: 37
l_displaced_atoms:
- molecule: Monomer
element: H
position: 38
- molecule: Monomer
element: H
position: 38
charge: 1
AA0170:
id: AA0170
name: L-glutamyl 5-glycerylphosphorylethanolamine
comments: 5-Glutamyl glycerylphosphorylethanolamine appears to occur uniquely
in translation elongation factor eEF-1 alpha chains. It is known to be a modification
of glutamic acid. The stereochemistry of the glycerol phosphate has not been
determined. The sn-3 form is shown. It has been established that is possible
for the glycerol group to be secondarily modified by conjugation with long chain
fatty acids, but probably not with inositol-containing lipids or glycolipids.
The predominant soluble form is not lipidated, and the modified protein does
not appear to be membrane associated.
synonyms:
- L-glutamyl 5-glycerylphosphorylethanolamine
- L-glutamyl 5-glycerophosphorylethanolamine
- (S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic
acid
- L-glutamyl 5-glycerophosphoethanolamine
identifiers:
- ns: go
id: GO:0018072
- ns: cas
id: 1190-00-7
- ns: mod
id: MOD:00179
- ns: resid
id: AA0170
structure: OC[C@H](COP(=O)(OCCNC(=O)CC[C@@H](C(=O)O)[NH3+])[O-])O
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 19
l_bond_atoms:
- molecule: Monomer
element: N
position: 22
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 21
- molecule: Monomer
element: H
position: 21
l_displaced_atoms:
- molecule: Monomer
element: H
position: 22
- molecule: Monomer
element: H
position: 22
charge: 1
AA0021:
id: AA0021
name: N-formyl-L-methionine
comments: "N-formylmethionine is translated for the initiator codon in bacteria,\
\ and there are different tRNA's with specific tRNA synthases for the initiator\
\ N-formylmethionine and the elongation methionine forms. In eukaryotic organelles\
\ there is only one tRNA for methionine. A portion of the Met-tRNA is N-formylated\
\ by mitochondrion specific methionyl-tRNA formyltransferase and recruited by\
\ mitochondrial translation initiation factor 2. As an aldehyde, the formyl\
\ group readily undergoes hydration. For the hydrated form N-(dihydroxymethyl)-L-methionine\
\ of this residue, see RESID:AA0493. Although appropriate, the keyword \"thioether\
\ bond\" normally does not appear for this amino acid. Generating Enzyme: methionine--tRNA\
\ ligase (EC 6.1.1.10); methionyl-tRNA formyltransferase (EC 2.1.2.9)."
synonyms:
- (2S)-2-formamido-4-methylsulfanyl-butanoic acid
- 2-formylamino-4-(methylthio)butanoic acid
- (2S)-2-formylamino-4-(methylsulfanyl)butanoic acid
- 2-formamido-4-(methylsulfanyl)butanoic acid
- M
- n-formylmethionine
- N-formyl-L-methionine
- 2-formylazanyl-4-(methylsulfanyl)butanoic acid
identifiers:
- ns: mod
id: MOD:00482
- ns: mod
id: MOD:00030
- ns: pdb.ligand
id: FME
- ns: resid
id: AA0021
- ns: pdb-ccd
id: FME
- ns: chebi
id: CHEBI:49298
- ns: cas
id: 4289-98-9
structure: CSCC[C@@H](C(=O)O)NC=O
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
AA0462:
id: AA0462
name: 3-hydroxy-L-phenylalanine
synonyms:
- beta-hydroxyphenylalanine
- beta-phenylserine
- 3-phenyl-L-serine
- 3-hydoxyphenylalanine
- (2S,3S)-2-amino-3-hydroxy-3-phenylpropanoic acid
- L-threo-3-phenylserine
identifiers:
- ns: chebi
id: CHEBI:16795
- ns: cas
id: 1078-17-7
- ns: resid
id: AA0462
- ns: mod
id: MOD:01385
structure: O[C@H]([C@@H](C(=O)O)N)c1ccccc1
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
- molecule: Monomer
element: H
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
AA0034:
id: AA0034
name: S-phospho-L-cysteine
synonyms:
- (2R)-2-amino-3-phosphonosulfanyl-propanoic acid
- S-phosphonocysteine
- S3-phosphocysteine
- C
- s-phosphocysteine
- 2-azanyl-3-(phosphonosulfanyl)propanoic acid
- S-phosphono-L-cysteine
- cysteine phosphate thioester
- (2R)-2-amino-3-(phosphonosulfanyl)propanoic acid
identifiers:
- ns: go
id: GO:0018218
- ns: pdb.ligand
id: CSP
- ns: resid
id: AA0034
- ns: chebi
id: CHEBI:61956
- ns: pdb-ccd
id: CSP
- ns: cas
id: 115562-30-6
- ns: mod
id: MOD:00043
structure: OC(=O)[C@H](CSP(=O)([O-])[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
AA0054:
id: AA0054
name: N-acetyl-L-valine
synonyms:
- (2S)-2-acetamido-3-methylbutanoic acid
- 2-acetylazanyl-3-methylbutanoic acid
- N-acetylvaline
- 2-acetylamino-3-methylbutanoic acid
identifiers:
- ns: mod
id: MOD:00063
- ns: chebi
id: CHEBI:21565
- ns: resid
id: AA0054
- ns: cas
id: 96-81-1
- ns: go
id: GO:0018001
structure: OC[C@H](C(C)C)NC(=O)C
base_monomers:
- V
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
AA0195:
id: AA0195
name: D-serine
comments: 'Generating Enzyme: protein-serine epimerase (EC 5.1.1.16).'
synonyms:
- (R)-2-amino-3-hydroxypropanoic acid
identifiers:
- ns: pdb.ligand
id: DSN
- ns: go
id: GO:0019126
- ns: chebi
id: CHEBI:29998
- ns: mod
id: MOD:00891
- ns: resid
id: AA0195
- ns: cas
id: 312-84-5
- ns: mod
id: MOD:00202
structure: OC[C@H](C(=O)O)[NH3+]
base_monomers:
- S
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
- molecule: Monomer
element: H
position: 7
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
AA0336:
id: AA0336
name: N-methyl-L-isoleucine
comments: 'This modification is predicted for proteins homologous to pilin in
certain organisms where the position corresponding to N-methylphenylalanine
instead encodes isoleucine. Polypeptides with monomethylated amino terminals
can undergo premature cleavage during the coupling step of an Edman degradation.
This can result in "preview" with both a residue and the following residue being
seen from the first step on through a sequence. Generating Enzyme: prepilin
peptidase (EC 3.4.23.43).'
synonyms:
- (2S,3S)-2-methylamino-3-methylpentanoic acid
- N-methylisoleucine
- n-methyl-isoleucine
- I
- N-methyl-L-isoleucine
- (2S,3S)-3-methyl-2-methylamino-pentanoic acid
identifiers:
- ns: cas
id: 4125-98-8
- ns: resid
id: AA0336
- ns: pdb.ligand
id: IML
- ns: mod
id: MOD:00341
- ns: go
id: GO:0046895
- ns: pdb-ccd
id: IML
structure: CC[C@@H]([C@@H](C(=O)O)[NH2+]C)C
base_monomers:
- I
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
AA0361:
id: AA0361
name: O-sulfo-L-serine
synonyms:
- O-sulfo-L-serine
- 2-amino-3-hydroxypropanoic acid 3-sulfate
- (2S)-2-amino-3-(sulfooxy)propanoic acid
- (2S)-2-amino-3-sulfooxy-propanoic acid
- serine sulfate ester
- S
- O3-sulfonoserine
- o-sulfo-l-serine
- O3-sulfoserine
identifiers:
- ns: pdb-ccd
id: OSE
- ns: mod
id: MOD:00366
- ns: pdb.ligand
id: OSE
- ns: resid
id: AA0361
- ns: cas
id: 626-69-7
- ns: go
id: GO:0050984
structure: OC(=O)[C@H](COS(=O)(=O)[O-])[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
AA0095:
id: AA0095
name: L-proline amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- L-prolinamide
- (2S)-pyrrolidine-2-carboxamide
- l-prolinamide
- P
- prolinamide
identifiers:
- ns: resid
id: AA0095
- ns: chebi
id: CHEBI:21374
- ns: go
id: GO:0018048
- ns: mod
id: MOD:00104
- ns: pdb-ccd
id: LPD
- ns: pdb.ligand
id: NH2
- ns: cas
id: 7531-52-4
structure: NC(=O)[C@@H]1CCC[NH2+]1
base_monomers:
- P
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0477:
id: AA0477
name: L-lysyl-poly(ADP-ribose)
comments: 'The alpha form is presented. The keyword "phosphoprotein" is not used
with ADP-ribosylation. Generating Enzyme: NAD+ ADP-ribosyltransferase (EC 2.4.2.30).'
synonyms:
- poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl]
(2S)-2,6-diaminohexanoate
identifiers:
- ns: cas
id: 26656-46-2
- ns: resid
id: AA0477
- ns: mod
id: MOD:01400
structure: '[NH3+]CCCC[C@@H](C(=O)O[C@H]1O[C@@H]([C@H]([C@H]1O)O)CO[P@](=O)(O[P@@](=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1NC=N[C@H]2N)[O-])[O-])[NH3+]'
base_monomers:
- K
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AA0342:
id: AA0342
name: 2-(S-L-cysteinyl)-D-allo-threonine
comments: The D-stereoisomer of the 2-S-cysteinyl substituted threonine has S
configuration. The second chiral center of the threonine is not inverted from
the L-threo diastereomer (J.C. Vederas, private communication, 2003), and is
thus D-allo.
synonyms:
- (2R,5S,6R)-2,5-diamino-5-carboxy-6-hydroxy-4-thiaheptanoic acid
- (2S,3R)-2-amino-2-[(2R)-2-amino-2-carboxyethyl]sulfanyl-3-hydroxybutanoic acid
- alpha-(L-cystein-S-yl)-D-allo-threonine
identifiers:
- ns: mod
id: MOD:00347
- ns: go
id: GO:0046926
- ns: resid
id: AA0342
structure: O=C[C@H](CS[C@](C(=O)O)([C@H](O)C)N)[NH3+]
base_monomers:
- T
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
AA0026:
id: AA0026
name: (2S,3R)-3-hydroxyasparagine
comments: 'This diastereomeric form has been found in the EGF domain of many proteins.
For the (2S,3S)-diastereomer, see RESID:AA0478. The PDB group code includes
models with both the (2S,3R) and the (2S,3S) stereoconfiguration. The Enzyme
Commission has not yet distinguished the different stereospecific enzyme activities.
Generating Enzyme: peptide-aspartate beta-dioxygenase (EC 1.14.11.16).'
synonyms:
- (3S)-3-hydroxy-L-asparagine
- (2S,3S)-2,4-diamino-3-hydroxy-4-oxo-butanoic acid
- (2S,3R)-2,4-diamino-3-hydroxy-4-oxobutanoic acid
- N
- 2-azanyl-3-hydroxy-4-butanediamic acid
- (2S,3R)-2-amino-3-hydroxy-4-butanediamic acid
- beta-hydroxyasparagine
- L-erythro-beta-hydroxyasparagine
identifiers:
- ns: resid
id: AA0026
- ns: cas
id: 20790-74-3
- ns: go
id: GO:0018376
- ns: mod
id: MOD:00035
- ns: pdb-ccd
id: AHB
- ns: pdb.ligand
id: AHB
structure: OC(=O)[C@H]([C@H](C(=O)N)O)N
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
AA0535:
id: AA0535
name: N,N,N-trimethyl-L-serine
comments: 'Consult FAQ at http://pir.georgetown.edu/resid/faq.shtml#q12 concerning
calculation of the difference formula. Generating Enzyme: N-terminal RCC1 methyltransferase
(EC 2.1.1.-).'
synonyms:
- (2S)-2-trimethylammonio-3-hydroxypropanoic acid
- (1S)-1-carboxy-2-hydroxy-N,N,N-trimethylethanazanium
- N,N,N-trimethylserinium
- N,N,N-trimethylserine cation
- (1S)-1-carboxy-2-hydroxy-N,N,N-trimethylethanaminium
identifiers:
- ns: go
id: GO:0035570
- ns: mod
id: MOD:01784
- ns: resid
id: AA0535
structure: OC[C@H]([N](C)(C)C)C(=O)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
- molecule: Monomer
element: H
position: 11
AA0498:
id: AA0498
name: O-cholinephosphoryl-L-serine
comments: In Neisseria this is produced as a secondary modification by methylation
of O-(2-aminoethylphosphoryl)-L-serine. See RESID:AA0497.
synonyms:
- serine choline phosphodiester
- serine choline phosphate
- 2-[([(2S)-2-amino-2-carboxyethoxy][hydroxy]phosphoryl)oxy]-N,N,N-trimethylethanaminium
- O3-phosphocholine-L-serine
- O3-[(2-[trimethylammonio]ethyl)phosphoryl]-L-serine
- 2-[([(2S)-2-azanyl-2-carboxyethoxy][hydroxy]phosphoryl)oxy]-N,N,N-trimethylethanazanium
identifiers:
- ns: mod
id: MOD:01588
- ns: resid
id: AA0498
structure: N[C@H](C(=O)O)CO[P@@](=O)(OCC[N](C)(C)C)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0053:
id: AA0053
name: N-acetyl-L-tyrosine
synonyms:
- 2-acetylamino-3-(4-hydoxyphenyl)propanoic acid
- 2-acetylazanyl-3-(4-hydoxyphenyl)propanoic acid
- N-acetyltyrosine
- N-acetyl-L-tyrosine
- (2S)-2-acetamido-3-(4-hydoxyphenyl)propanoic acid
- Y
- n-acetyl-l-tyrosine
- (2S)-2-acetamido-3-(4-hydroxyphenyl)propanoic acid
identifiers:
- ns: chebi
id: CHEBI:21563
- ns: mod
id: MOD:00062
- ns: pdb-ccd
id: 3NF
- ns: resid
id: AA0053
- ns: go
id: GO:0018000
- ns: cas
id: 537-55-3
structure: OC(=O)[C@H](Cc1ccc(cc1)O)NC(=O)C
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
AA0122:
id: AA0122
name: L-2-aminoadipic acid
comments: 'The oxidation of allysine to 2-aminoadipic acid is not well characterized.
Generating Enzyme: protein-lysine 6-oxidase (EC 1.4.3.13).'
synonyms:
- (2S)-2-aminohexanedioic acid
- 2-aminohexanedioic acid
- L-alpha-aminoadipic acid
- 2-amino-1,4-butanedicarboxylic acid
- X
identifiers:
- ns: resid
id: AA0122
- ns: cas
id: 1118-90-7
- ns: mod
id: MOD:00131
- ns: pdb-ccd
id: UN1
- ns: go
id: GO:0019728
structure: O=C[C@H](CCCC(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
AA0359:
id: AA0359
name: 5-hydroxy-N6,N6,N6-trimethyl-L-lysine
comments: Hydroxylation at C-5 is assumed. Neither the position of the hydroxylation
nor the stereochemistry for the second chiral center it produces have been determined.
The (2S,5R) diastereomer is shown. Consult FAQ at http://pir.georgetown.edu/resid/faq.shtml#q12
concerning calculation of the difference formula.
synonyms:
- (2Xi,5S)-5-azanyl-5-carboxy-2-hydroxy-N,N,N-trimethylpentanazanium
- alpha-amino-epsilon-dimethylamino-delta-hydroxycaproic acid
- delta-hydroxy-epsilon-N,N,N-trimethyllysine
- 5-hydroxy-N(zeta)-trimethyllysine
- (2R,5Xi)-5-amino-5-carboxy-2-hydroxy-N,N,N-trimethylpentan-1-aminium
- 5-hydroxy-N6,N6,N6-trimethyllysine cation
- lysine derivative Lys(z)
- (2Xi,5S)-5-amino-5-carboxy-2-hydroxy-N,N,N-trimethylpentanaminium
- 5-hydroxy-N6,N6,N6-trimethyllysin-N6-ium
identifiers:
- ns: mod
id: MOD:00364
- ns: resid
id: AA0359
- ns: go
id: GO:0050838
structure: O[C@@H](C[N](C)(C)C)CC[C@@H](C(=O)O)N
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
AA0035:
id: AA0035
name: 1'-phospho-L-histidine
comments: 'In the older biochemical literature this is usually called histidine-3-phosphate.
See also RESID:AA0036. The crystallographic designation for the substituted
nitrogen is epsilon-2, E2. Generating Enzyme: protein-histidine tele-kinase
(EC 2.7.3.12).'
synonyms:
- tele-phosphohistidine
- N1-phosphonohistidine
- n1-phosphonohistidine
- histidine-N(epsilon)-phosphate
- H
- (2S)-2-amino-3-(1-phosphono-1H-imidazol-4-yl)propanoic acid
- NE2-phosphonohistidine
- histidine-N1'-phosphate
- (2S)-2-amino-3-(1-phosphonoimidazol-4-yl)propanoic acid
- 1-phosphono-L-histidine
- N(tau)-phosphohistidine
- histidine-3-phosphate [misnomer]
- 2-azanyl-3-(1-phosphono-1H-imidazol-4-yl)propanoic acid
identifiers:
- ns: resid
id: AA0035
- ns: pdb-ccd
id: NEP
- ns: go
id: GO:0018106
- ns: cas
id: 5789-14-0
- ns: pdb.ligand
id: NEP
- ns: mod
id: MOD:00044
structure: OC(=O)[C@@H](Cc1ncn(c1)P(=O)([O-])[O-])[NH3+]
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0540:
id: AA0540
name: L-cysteine 3-hydroxypyridine-2,5-dicarboxylic acid
comments: Formed by the metathesis of two didehydroalanines made from serines,
condensation with a cysteine carbonyl and dehydrogenation. This modification
is currently represented in the PDB as part of the HET group for the entire
molecule of nosiheptide.
synonyms:
- 6-[(1R)-1-amino-2-sulfanylethyl]-3-hydroxypyridine-2,5-dicarboxylic acid
- 6-[1-azanyl-2-sulfanylethyl]-3-hydroxypyridine-2,5-dicarboxylic acid
identifiers:
- ns: pdb.ligand
id: MH6
- ns: resid
id: AA0540
- ns: mod
id: MOD:01814
structure: SC[C@H](c1nc(C(=O)O)c(cc1C=O)[O-])[NH3+]
base_monomers:
- S
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
AA0510:
id: AA0510
name: 3',5'-diiodo-L-tyrosine
synonyms:
- 3,5-diiodotyrosine
- 3,5-diiodo-L-tyrosine
- iodogorgoic acid
- (2S)-2-amino-3-(4-hydroxy-3,5-diiodophenyl)propanoic acid
- Y
- DIT
- (2S)-2-amino-3-(4-hydroxy-3,5-diiodo-phenyl)propanoic acid
identifiers:
- ns: resid
id: AA0510
- ns: pdb.ligand
id: TYI
- ns: mod
id: MOD:01613
- ns: cas
id: 300-39-0
- ns: pdb-ccd
id: TYI
- ns: chebi
id: CHEBI:15768
structure: '[NH3+][C@H](C(=O)O)Cc1cc(I)c(c(c1)I)[O-]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AA0097:
id: AA0097
name: L-threonine amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- (2s,3r)-2-amino-3-hydroxy-butanamide
- (2S,3R)-2-amino-3-hydroxybutanamide
- (2S,3R)-2-amino-3-hydroxy-butanamide
- threoninamide
identifiers:
- ns: go
id: GO:0018050
- ns: resid
id: AA0097
- ns: mod
id: MOD:00106
- ns: pdb-ccd
id: 9AT
- ns: cas
id: 2280-40-2
- ns: chebi
id: CHEBI:21404
- ns: pdb.ligand
id: NH2
structure: C[C@H]([C@H]([NH3+])C(=O)N)O
base_monomers:
- T
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
AA0055:
id: AA0055
name: N6-acetyl-L-lysine
comments: 'Generating Enzyme: histone acetyltransferase (EC 2.3.1.48); tubulin
N-acetyltransferase (EC 2.3.1.108); protein lysine N6-acetyltransferase (EC
2.3.1.-).'
synonyms:
- N~6~-acetyl-L-lysine
- n(6)-acetyllysine
- (2S)-6-acetamido-2-aminohexanoic acid
- 6-acetylazanyl-2-aminohexanoic acid
- N(zeta)-acetyllysine
- K
- 6-acetylamino-2-aminohexanoic acid
- epsilon-acetyllysine
- (2S)-6-acetamido-2-amino-hexanoic acid
identifiers:
- ns: chebi
id: CHEBI:61930
- ns: pdb-ccd
id: ALY
- ns: mod
id: MOD:00064
- ns: resid
id: AA0055
- ns: pdb.ligand
id: ALY
- ns: go
id: GO:0018003
- ns: cas
id: 692-04-6
structure: CC(=O)NCCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
AA0052:
id: AA0052
name: N-acetyl-L-threonine
synonyms:
- 2-acetylamino-3-hydroxybutanoic acid
- n-methylcarbonylthreonine
- (2S,3R)-2-acetamido-3-hydroxy-butanoic acid
- T
- N-methylcarbonylthreonine
- 2-acetylazanyl-3-hydroxybutanoic acid
- N-acetyl-L-threonine
- (2S,3R)-2-acetamido-3-hydroxybutanoic acid
- N-acetylthreonine
identifiers:
- ns: resid
id: AA0052
- ns: cas
id: 17093-74-2
- ns: go
id: GO:0017199
- ns: mod
id: MOD:00061
- ns: pdb-ccd
id: THC
- ns: chebi
id: CHEBI:45826
structure: CC(=O)N[C@H](C(=O)O)[C@H](O)C
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
AA0093:
id: AA0093
name: L-methionine amide
comments: 'Although appropriate, the keyword "thioether bond" normally does not
appear for this amino acid. Generating Enzyme: peptidylglycine monooxygenase
(EC 1.14.17.3).'
synonyms:
- 2-amino-4-(methylthio)butanamide
- methioninamide
- (2S)-2-amino-4-(methylsulfanyl)butanamide
identifiers:
- ns: cas
id: 4510-08-1
- ns: chebi
id: CHEBI:21362
- ns: mod
id: MOD:00102
- ns: go
id: GO:0018046
- ns: resid
id: AA0093
- ns: pdb.ligand
id: NH2
structure: CSCC[C@H]([NH3+])C(=O)N
base_monomers:
- M
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
AA0499:
id: AA0499
name: O-2,4-diacetamido-2,4-dideoxyglucosyl-L-serine
comments: It is not clear whether or not there is a chemical difference in the
glycosylation of the two varieties of strain MS11 used in these experiments.
For O-(2,4-diacetamido-2,4,6-trideoxy-D-glucosyl)-L-serine, see RESID:AA0607.
synonyms:
- O-(2,4-diacetamido-2,4-dideoxy-beta-D-glucopyranosyl)-L-serine
- (2S)-2-amino-3-[(2,4-diacetamido-2,4-dideoxy-beta-D-glucopyranosyl)oxy]propanoic
acid
- O3-(2,4-diacetamido-2,4-dideoxy-beta-D-glucopyranosyl)-L-serine
- O-seryl-beta-2,4-bis(acetylamino)glucoside
- O-[2,4-bis(acetylamino)]glucosyl-L-serine
- DADDGlc
identifiers:
- ns: pdb.ligand
id: DT6
- ns: mod
id: MOD:01589
- ns: resid
id: AA0499
structure: OC[C@H]1O[C@@H](OC[C@@H](C(=O)O)[NH3+])[C@@H]([C@H]([C@@H]1NC(=O)C)O)NC(=O)C
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0538:
id: AA0538
name: N,N-dimethyl-L-leucine
synonyms:
- (2S)-2-(dimethylamino)-4-methylpentanoic acid
- 2-(dimethylazanyl)-4-methylpentanoic acid
- N,N-dimethylleucine
- 2-(dimethylamino)-4-methylvaleric acid
identifiers:
- ns: resid
id: AA0538
- ns: mod
id: MOD:01806
structure: CC(C[C@H]([NH+](C)C)C(=O)O)C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
AA0532:
id: AA0532
name: N6-butanoyl-L-lysine
comments: A metabolic source for butanoic acid in the nucleus is not evident,
and a responsible generating enzyme activity is not identified.
synonyms:
- N6-butyryllysine
- (2S)-2-amino-6-(butanoylamino)hexanoic acid
- epsilon-butyryl-L-lysine
- N(zeta)-butanoyllysine
- 2-amino-6-butyrylaminocaproic acid
- (2S)-2-azanyl-6-(butanoylamino)hexanoic acid
- n~6~-butanoyl-l-lysine
- N~6~-butanoyl-L-lysine
- N6-(1-oxobutyl)-L-lysine
- epsilon-butanoyl-L-lysine
identifiers:
- ns: resid
id: AA0532
- ns: mod
id: MOD:01781
- ns: pdb.ligand
id: BTK
- ns: pdb-ccd
id: BTK
structure: CCCC(=O)NCCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0332:
id: AA0332
name: S-carbamoyl-L-cysteine
comments: This modification can undergo dehydration to produce S-cyanocysteine.
See RESID:AA0333. Carbamoylation of the sulfhydryl group can be artifactual,
in particular when urea buffers are used.
synonyms:
- S-(aminocarbonyl)cysteine
- S-cysteinyl carbamate ester
- (2R)-3-aminocarbonylsulfanyl-2-azanyl-propanoic acid
- beta-carbamylthioalanine
- S-carbamylcysteine
- S-carbamoyl-L-cysteine
- 2-amino-3-(aminocarbonyl)thiopropanoic acid
- S-carbamoylcysteine
- s-carbamoyl-l-cysteine
- C
- 2-amino-3-(aminocarbonyl)sulfanylpropanoic acid
- alpha-amino-beta-carbamylthiopropionic acid
- (R)-2-amino-3-(carbamoylsulfanyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: QCS
- ns: resid
id: AA0332
- ns: go
id: GO:0046891
- ns: cas
id: 2072-71-1
- ns: mod
id: MOD:00337
structure: NC(=O)SC[C@@H](C(=O)O)N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
AA0543:
id: AA0543
name: 2'-oxo-L-tryptophan
comments: This modification, which is not observed in other preparations of the
same protein, is probably produced artifactually.
synonyms:
- W
- 2-hydroxy-tryptophan
- 2-oxotryptophan
- 2-azanyl-3-[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]propanoic acid
- 2-hydroxy-L-tryptophan
- (2S)-2-amino-3-(2-hydroxy-1H-indol-3-yl)propanoic acid
- 2-oxo-L-tryptophan
- (2S)-2-amino-3-[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]propanoic acid
identifiers:
- ns: pdb.ligand
id: TRO
- ns: mod
id: MOD:01817
- ns: pdb-ccd
id: TRO
- ns: resid
id: AA0543
structure: OC(=O)[C@H](C[C@@H]1C(=O)Nc2c1cccc2)[NH3+]
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0475:
id: AA0475
name: N6-propanoyl-L-lysine
comments: 'A metabolic source for propanoic acid in the nucleus is not evident;
the modification would be isobaric with lactaldehyde adduct, an advanced glycation
end product of artifactual nucleic acid degradation This modification has been
shown to be produced by Gcn-5-related N-acetyltransferases in some bacterial
systems. In eukaryotes, a metabolic source for propanoic acid in the nucleus
is not evident, and a responsible generating enzyme activity is not identified.
Generating Enzyme: lysine N6-acyltransferase, acetoin utilization protein AcuA
(EC 2.3.1.-).'
synonyms:
- N6-propionyllysine
- (2S)-2-amino-6-(propanoylamino)hexanoic acid
- N~6~-propanoyl-L-lysine
- 2-amino-6-propionylaminocaproic acid
- (2S)-2-azanyl-6-(propanoylamino)hexanoic acid
- N6-(1-oxopropyl)-L-lysine
- epsilon-propionyl-L-lysine
- N(zeta)-propanoyllysine
- n~6~-propanoyl-l-lysine
- epsilon-propanoyl-L-lysine
identifiers:
- ns: resid
id: AA0475
- ns: pdb-ccd
id: PRK
- ns: pdb.ligand
id: PRK
- ns: cas
id: 1974-17-0
- ns: mod
id: MOD:01398
structure: CCC(=O)NCCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0352:
id: AA0352
name: 1'-(8alpha-FMN)-L-histidine
comments: 'The arrangement of the attachment has not been completely established
in some cases. The keyword "phosphoprotein" is not used with flavin modifications
linked through the flavin. Generating Enzyme: autocatalytic.'
synonyms:
- 8alpha-(N(epsilon)-histidyl)FMN
- 8alpha-(N1'-histidyl)FMN
- (S)-2-amino-3-(1-[8alpha riboflavin 5'-dihydrogen phosphate]imidazol-4-yl)propanoic
acid
- N(tau)-(8alpha-FMN)-histidine
- tele-(8alpha-FMN)-histidine
identifiers:
- ns: mod
id: MOD:00357
- ns: go
id: GO:0050743
- ns: resid
id: AA0352
structure: O=c1[nH]c(=O)c2c([nH]1)n(C[C@@H]([C@@H]([C@@H](COP(=O)([O-])[O-])O)O)O)c1=C[C@H](C(=Cc1n2)C)Cn1cnc(c1)C[C@@H](C(=O)O)[NH3+]
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 46
l_bond_atoms:
- molecule: Monomer
element: N
position: 49
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 48
- molecule: Monomer
element: H
position: 48
l_displaced_atoms:
- molecule: Monomer
element: H
position: 49
- molecule: Monomer
element: H
position: 49
charge: 1
AA0625:
id: AA0625
name: 2-(L-cystein-S-yl)-L-threonine
synonyms:
- (2R,3R)-2-amino-2-[(2R)-2-amino-2-carboxyethyl]sulfanyl-3-hydroxybutanoic acid
- (2R,5R,6R)-2,5-diamino-5-carboxy-6-hydroxy-4-thiaheptanoic acid
- alpha-(L-cystein-S-yl)-L-threonine
identifiers:
- ns: mod
id: MOD:01988
- ns: resid
id: AA0625
structure: O=C[C@H](CS[C@@](C(=O)O)([C@H](O)C)N)[NH3+]
base_monomers:
- T
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
AA0405:
id: AA0405
name: O-fucosyl-L-threonine
comments: 'See also RESID:AA0155, RESID:AA0247, RESID:AA0399, RESID:AA0401, RESID:AA0403,
and RESID:AA0515 for other O-glycosylated threonines. Generating Enzyme: peptide-O-fucosyltransferase
(EC 2.4.1.221).'
synonyms:
- O3-fucosylthreonine
- O-glycosylthreonine
- (2S,3R)-2-amino-3-(6-deoxy-alpha-D-galactopyranosyloxy)butanoic acid
identifiers:
- ns: resid
id: AA0405
- ns: mod
id: MOD:00813
structure: OC(=O)[C@H]([C@H](O[C@H]1O[C@H](C)[C@@H]([C@@H]([C@H]1O)O)O)C)[NH3+]
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 25
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 25
- molecule: Monomer
element: H
position: 25
charge: 1
AA0397:
id: AA0397
name: O-glucosyl-L-serine
comments: See also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291,
RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402,
RESID:AA0404, RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines.
synonyms:
- (2S)-2-amino-3-(beta-D-glucopyranosyloxy)propanoic acid
- O3-glucosylserine
- O-glycosylserine
identifiers:
- ns: mod
id: MOD:00804
- ns: resid
id: AA0397
structure: OC[C@H]1O[C@H](OC[C@@H](C(=O)O)[NH3+])[C@@H]([C@H]([C@@H]1O)O)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0121:
id: AA0121
name: L-allysine
comments: 'Generating Enzyme: protein-lysine 6-oxidase (EC 1.4.3.13).'
synonyms:
- 2-aminoadipate 6-semialdehyde
- AASA
- alpha-amino-adipic acid delta-semialdahyde
- (2S)-2-amino-6-oxohexanoic acid
- 6-oxonorleucine
- 2-amino-5-formylvaleric acid
- 2-amino-adipic acid semialdahyde
- 5-formyl-norvaline
identifiers:
- ns: resid
id: AA0121
- ns: cas
id: 1962-83-0
- ns: chebi
id: CHEBI:17917
- ns: mod
id: MOD:00130
- ns: go
id: GO:0018057
structure: O=CCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
AA0467:
id: AA0467
name: L-valine thiazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-cysteine
cyclase (EC 4.2.1.-); peptidyl-thiazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-[(1S)-1-amino-2-methylpropyl]-1,3-thiazole-4-carboxylic acid
- 2-[1-azanyl-2-methylpropyl]-1,3-thiazole-4-carboxylic acid
identifiers:
- ns: mod
id: MOD:01390
- ns: pdb.ligand
id: BB9
- ns: resid
id: AA0467
structure: '[NH3+][C@H](c1scc(n1)C(=O)O)C(C)C'
base_monomers:
- V
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
AA0061:
id: AA0061
name: N-methyl-L-alanine
comments: 'Polypeptides with monomethylated amino terminals can undergo premature
cleavage during the coupling step of an Edman degradation. This can result in
"preview" with both a residue and the following residue being seen from the
first step on through a sequence. Generating Enzyme: N-terminal RCC1 methyltransferase
(EC 2.1.1.-).'
synonyms:
- n-methyl-l-alanine
- (2S)-2-(methylamino)propanoic acid
- (2S)-2-methylaminopropanoic acid
- N-methyl-L-alanine
- A
- N-methylalanine
- 2-methylazanylpropanoic acid
identifiers:
- ns: resid
id: AA0061
- ns: cas
id: 3913-67-5
- ns: mod
id: MOD:00070
- ns: pdb-ccd
id: MAA
- ns: chebi
id: CHEBI:61922
- ns: pdb.ligand
id: MAA
- ns: go
id: GO:0018011
structure: C[C@H]([NH2+]C)C(=O)O
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
- molecule: Monomer
element: H
position: 4
charge: 1
AA0548:
id: AA0548
name: S-(2-aminovinyl)-L-cysteine
comments: 'This cross-link arises from the decarboxylation of the carboxyl-terminal
portion of a lanthionine, either L-lanthionine (see RESID:AA0110) or meso-lanthionine
(see RESID:AA0111). The stereochemistry of the (2-aminovinyl)-cysteine in cypemycin
has not been determined. For the D stereoisomer, see RESID:AA0204. Generating
Enzyme: peptidyl-cysteine dethiolase (EC 4.4.1.-); peptidyl-cysteine dehydroalanine/dehydrobutyrine
ligase (EC 6.2.-.-).'
synonyms:
- (2R)-2-amino-3-([(Z)-2-aminoethenyl]sulfanyl)propanoic acid
- (R,Z)-S-(2-aminovinyl)cysteine
identifiers:
- ns: resid
id: AA0548
- ns: mod
id: MOD:01842
structure: N/C=C\SC[C@@H]([NH3+])C(=O)O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
AA0257:
id: AA0257
name: N-(L-glutamyl)-L-tyrosine
comments: 'Generating Enzyme: tubulin--tyrosine ligase (EC 6.3.2.25).'
synonyms:
- (S,S)-2-(2-aminopentanedio-1-yl)amino-3-(4-hydoxyphenyl)propanoic acid
- N-(L-glutamyl)-L-tyrosine
identifiers:
- ns: mod
id: MOD:00262
- ns: go
id: GO:0018166
- ns: chebi
id: CHEBI:21477
- ns: resid
id: AA0257
structure: '[O-]C(=O)CC[C@@H](C(=O)N[C@H](C(=O)[O-])Cc1ccc(cc1)O)[NH3+]'
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
AA0173:
id: AA0173
name: L-bromohistidine
comments: The position of the bromine substitution is uncertain. The 2'-bromohistidine
is shown.
identifiers:
- ns: mod
id: MOD:00182
- ns: resid
id: AA0173
- ns: go
id: GO:0018074
structure: OC(=O)[C@@H]([NH3+])Cc1cnc([nH]1)Br
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
AA0148:
id: AA0148
name: L-tryptophyl quinone
synonyms:
- 3-(6,7-dioxo-6,7-dihydro-1H-indol-3-yl)-L-alanine
- 3-[(2S)-2-amino-2-carboxyethyl]-6,7-indolinedione
- 2-amino-3-(6,7-dioxo-6,7-dihydro-1h-indol-3-yl)-propionic acid
- 2-amino-3-(6,7-dioxo-6,7-dihydro-1H-indol-3-yl)-propionic acid
- W
- N-(3-carboxy-1-oxopropyl)-L-tryptophan
- (2S)-2-amino-3-(6,7-dioxo-1H-indol-3-yl)propanoic acid
identifiers:
- ns: resid
id: AA0148
- ns: mod
id: MOD:00157
- ns: pdb.ligand
id: TRQ
- ns: cas
id: 73205-73-9
- ns: go
id: GO:0019926
- ns: pdb-ccd
id: TRQ
structure: OC(=O)[C@H](Cc1c[nH]c2c1C=CC(=O)C2=O)[NH3+]
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
AA0391:
id: AA0391
name: 2-(S-L-cysteinyl)pyruvic acid O-phosphothioketal
comments: 'Generating Enzyme: 3-phosphoshikimate 1-carboxyvinyltransferase (EC
2.5.1.19); UDP-N-acetylglucosamine 1-carboxyvinyltransferase (EC 2.5.1.7).'
synonyms:
- s-[(1s)-1-carboxy-1-(phosphonooxy)ethyl]-l-cysteine
- (2S)-2-[(2R)-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-2-phosphonooxy-propanoic
acid
- cysteinyl pyruvate O-phosphothioketal
- (2R)-2-amino-3-[1-carboxy-1-(phosphonooxy)ethyl]sulfanylpropanoic acid
- phosphoenolpyruvate cysteine adduct
- C
- 2-([(2R)-2-azanyl-2-carboxyethyl]sulfanyl)-2-(phosphonooxy)propanoic acid
- S-[1-carboxy-1-(phosphonooxy)ethyl]cysteine
- S-[(1S)-1-carboxy-1-(phosphonooxy)ethyl]-L-cysteine
- phospholactoyl cysteine adduct
- 2-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-2-(phosphonooxy)propanoic acid
identifiers:
- ns: mod
id: MOD:00797
- ns: resid
id: AA0391
- ns: pdb.ligand
id: QPA
- ns: pdb-ccd
id: QPA
structure: O=C[C@H](CS[C@@](C(=O)[O-])(OP(=O)([O-])[O-])C)[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
AA0027:
id: AA0027
name: (2S,3R)-3-hydroxyaspartic acid
comments: 'This diastereomeric form has been found in the EGF domain of many proteins.
For the (2S,3S)-diastereomer, see RESID:AA0579. The Enzyme Commission has not
yet distinguished the different stereospecific enzyme activities. Generating
Enzyme: peptide-aspartate beta-dioxygenase (EC 1.14.11.16).'
synonyms:
- D
- (3r)-3-hydroxy-l-aspartic acid
- L-erythro-beta-hydroxyaspartic acid
- 2-amino-3-hydroxysuccinic acid
- (2S,3R)-2-amino-3-hydroxybutanedioic acid
- (3R)-3-hydroxy-L-aspartic acid
- 3-hydroxyaspartic acid
- (2S,3R)-2-azanyl-3-hydroxy-butanedioic acid
- 2-azanyl-3-hydroxybutanedioic acid
identifiers:
- ns: resid
id: AA0027
- ns: pdb.ligand
id: BH2
- ns: pdb-ccd
id: BH2
- ns: mod
id: MOD:00036
- ns: go
id: GO:0019715
structure: O=C[C@H]([C@H](C(=O)[O-])O)[NH3+]
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
AA0459:
id: AA0459
name: 5'-(L-tyros-5'-yl)amino-L-tyrosine
comments: This structure represents the cross-linked tyrosine portion of a four
residue bis(lysine tyrosylquinone) structure which is itself part of a zinc
binding complex with two histidine residues. This modification in the modeled
protein has not been chemically confirmed.
synonyms:
- 5'-[(tyros-5'-yl)amino]tyrosine
- 3-amino-l-tyrosine
- 5'-tyrosyl-5'-aminotyrosine
- bis(LTQ) linkage
- (2S)-2-amino-3-(3-amino-4-hydroxy-phenyl)propanoic acid
- (2S,2'S)-3,3'-[iminobis(4-hydroxybenzene-3,1-diyl)]bis(2-aminopropanoic acid)
- Y
- 3-amino-L-tyrosine
identifiers:
- ns: pdb.ligand
id: TY2
- ns: mod
id: MOD:01787
- ns: pdb-ccd
id: TY2
- ns: resid
id: AA0459
structure: OC[C@H](Cc1ccc(c(c1)Nc1cc(C[C@@H](CO)[NH3+])ccc1O)O)[NH3+]
base_monomers:
- Y
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
AA0456:
id: AA0456
name: N,N,N-trimethyl-L-methionine
comments: 'Although appropriate, the keyword "thioether bond" normally does not
appear for this amino acid. Consult FAQ at http://pir.georgetown.edu/resid/faq.shtml#q12
concerning calculation of the difference formula. Generating Enzyme: ribosomal
protein L11 methyltransferase (EC 2.1.1.-).'
synonyms:
- (1S)-1-carboxy-N,N,N-trimethyl-3-(methylsulfanyl)propanazanium
- N,N,N-trimethylmethioninium
- trimethyl-[(2S)-4-methylsulfanyl-1-oxidanyl-1-oxidanylidene-butan-2-yl]azanium
- (1S)-1-carboxy-N,N,N-trimethyl-3-(methylsulfanyl)propan-1-aminium
- 2-trimethylammonio-4-(methylthio)butanoic acid
- n,n,n-trimethylmethionine
- N,N,N-trimethylmethionine cation
- (1S)-1-carboxy-N,N,N-trimethyl-3-(methylsulfanyl)propanaminium
identifiers:
- ns: go
id: GO:0018014
- ns: mod
id: MOD:01382
- ns: resid
id: AA0456
- ns: pdb.ligand
id: 4MM
- ns: pdb-ccd
id: 4MM
structure: CSCC[C@H]([N](C)(C)C)C(=O)O
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
AA0192:
id: AA0192
name: D-allo-isoleucine
comments: 'Generating Enzyme: protein-isoleucine 2-epimerase (EC 5.1.1.-).'
synonyms:
- 2-azanyl-3-methylpentanoic acid
- alpha-amino-beta-methylvaleric acid
- D-threo-isoleucine
- 3-methyl-norvaline
- (2R,3S)-2-amino-3-methylpentanoic acid
- allo-D-isoleucine
identifiers:
- ns: pdb.ligand
id: DIL
- ns: go
id: GO:0019124
- ns: chebi
id: CHEBI:30007
- ns: cas
id: 1509-35-9
- ns: resid
id: AA0192
- ns: mod
id: MOD:00199
structure: CC[C@@H]([C@H](C(=O)O)[NH3+])C
base_monomers:
- I
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
AA0596:
id: AA0596
name: O-(L-isoglutamyl)-L-threonine
comments: 'Generating Enzyme: protein-glutamine gamma-glutamyltransferase (EC
2.3.2.13).'
synonyms:
- (gamma-glutamyl)histamine
- (2S)-2-amino-5-([2-(1H-imidazol-5-yl)ethyl]amino)-5-oxopentanoic acid
identifiers:
- ns: resid
id: AA0596
- ns: mod
id: MOD:01950
structure: O=C(CC[C@@H](C(=O)O)[NH3+])NCCc1cnc[nH]1
base_monomers:
- Q
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
AA0207:
id: AA0207
name: S-4-hydroxycinnamyl-L-cysteine
synonyms:
- (2R)-2-amino-3-([(2E)-3-(4-hydroxyphenyl)prop-2-enoyl]sulfanyl)propanoic acid
- cinnamate cysteine thioester
- S-para-coumaryl-L-cysteine
identifiers:
- ns: resid
id: AA0207
- ns: mod
id: MOD:00212
- ns: go
id: GO:0018097
- ns: pdb.ligand
id: HC4
structure: O=C(/C=C/c1ccc(cc1)O)SC[C@@H](C(=O)O)N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
- molecule: Monomer
element: H
position: 18
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
AA0085:
id: AA0085
name: L-cysteine amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- L-cysteinamide
- 2-amino-3-mercapto-propionamide
- cysteinamide
- (2R)-2-amino-3-sulfanylpropanamide
- C
- (2R)-2-amino-3-sulfanyl-propanamide
- 2-amino-3-mercaptopropanamide
identifiers:
- ns: mod
id: MOD:00094
- ns: cas
id: 74401-72-2
- ns: pdb-ccd
id: CY3
- ns: resid
id: AA0085
- ns: go
id: GO:0018038
- ns: pdb.ligand
id: CY3
- ns: chebi
id: CHEBI:21262
structure: NC(=O)[C@@H]([NH3+])CS
base_monomers:
- C
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0422:
id: AA0422
name: O-(N-acetylamino)fucosyl-L-serine
comments: See also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291,
RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402,
RESID:AA0404, and RESID:AA0406 for other O-glycosylated serines.
synonyms:
- (2S)-2-amino-3-(2-acetamido-2-deoxy-beta-D-fucopyranosyloxy)propanoic acid
- O3-(N-acetylfucosaminyl)serine
- O-(N-acetylfucosaminyl)serine
- O-(2-acetylamino-2-deoxy-beta-D-fucopyranosyl)-L-serine
- O3-(2-acetamido-2-deoxy-beta-D-fucopyranosyl)-L-serine
- O-seryl-beta-N-acetylfucosaminide
identifiers:
- ns: mod
id: MOD:00834
- ns: resid
id: AA0422
structure: CC(=O)N[C@H]1[C@H](OC[C@@H](C(=O)O)[NH3+])O[C@@H]([C@@H]([C@@H]1O)O)C
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
- molecule: Monomer
element: H
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0450:
id: AA0450
name: 2'-methylsulfonyl-L-tryptophan
comments: In virotoxin this modified tryptophan is formed after a 2'-(S-cysteinyl)tryptophan
crosslink is broken.
synonyms:
- 2-methylsulfonyl-3-((2S)-2-amino-2-carboxyethyl)-1H-indole
identifiers:
- ns: mod
id: MOD:01379
- ns: resid
id: AA0450
structure: OC(=O)[C@H](Cc1c2ccccc2[nH]c1S(=O)(=O)C)[NH3+]
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
AA0077:
id: AA0077
name: N6-palmitoyl-L-lysine
comments: 'Generating Enzyme: peptidyl-lysine N6-palmitoyltransferase (EC 2.3.1.-).'
synonyms:
- N6-(1-oxohexadecyl)-L-lysine
- epsilon-palmitoyllysine
- N(zeta)-palmitoyllysine
- (2S)-2-amino-6-(hexadecanoylamino)hexanoic acid
- 2-amino-6-(hexadecanamido)hexanoic acid
identifiers:
- ns: go
id: GO:0018029
- ns: cas
id: 559012-43-0
- ns: resid
id: AA0077
- ns: mod
id: MOD:00086
- ns: chebi
id: CHEBI:21895
structure: CCCCCCCCCCCCCCCC(=O)NCCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 25
l_bond_atoms:
- molecule: Monomer
element: N
position: 28
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 27
- molecule: Monomer
element: H
position: 27
l_displaced_atoms:
- molecule: Monomer
element: H
position: 28
- molecule: Monomer
element: H
position: 28
charge: 1
K, Y:
id: AA0233
name: 2'-(L-lys-N6-yl)-L-4',5'-topaquinone
comments: The linkage between the two components has not been established with
certainty. The relation of this cofactor to the copper binding site has not
been established.
synonyms:
- lysyl oxidase cofactor
- 1-[(S)-5-amino-5-carboxypentyl]amino-2-[(S)-2-amino-2-carboxyethyl]-2,6-cyclohexadien-4,5-dione
- 2'-(L-lysine)-L-tyrosyl-4',5'-quinone
- LTQ
identifiers:
- ns: go
id: GO:0018124
- ns: resid
id: AA0233
- ns: mod
id: MOD:00238
structure: O=C[C@H](CCCCNC1=CC(=O)C(=O)C=C1C[C@@H](C(=O)O)[NH3+])[NH3+]
base_monomers:
- K
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 21
l_bond_atoms:
- molecule: Monomer
element: N
position: 24
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 23
- molecule: Monomer
element: H
position: 23
l_displaced_atoms:
- molecule: Monomer
element: H
position: 24
- molecule: Monomer
element: H
position: 24
charge: 1
AA0094:
id: AA0094
name: L-phenylalanine amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- phenylalaninamide
- (2S)-2-amino-3-phenyl-propanamide
- phenylalanine amide
- F
- L-phenylalaninamide
- (2S)-2-amino-3-phenylpropanamide
identifiers:
- ns: chebi
id: CHEBI:21371
- ns: go
id: GO:0018047
- ns: cas
id: 5241-58-7
- ns: mod
id: MOD:00103
- ns: pdb.ligand
id: NFA
- ns: resid
id: AA0094
- ns: pdb-ccd
id: NFA
structure: '[NH3+][C@H](C(=O)N)Cc1ccccc1'
base_monomers:
- F
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
A, N:
id: AA0515
name: alanine isoaspartyl cyclopeptide
comments: This is a proposed cyclization between asparagine and the free amino
group of the preceding amino acid in a peptide. It is more probable that asparagine
cyclizes with the amino group of the following glycine, see RESID:AA0441.
synonyms:
- (2S,5S)-2-methyl-3,7-dioxo-1,4-diazepane-5-carboxylic acid
- 1,4.2-anhydro(L-alanyl-L-aspartic acid)
identifiers:
- ns: mod
id: MOD:01618
- ns: resid
id: AA0515
structure: OC[C@@H]1CC(=O)N[C@H](C(=O)N1)C
base_monomers:
- N
- A
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
I, T:
id: AA0472
name: 4-(1-hydroxyethyl)-7-isoleucino-2-(threonin-O3-ylcarbonyl)-7,8-dihydroquinolin-8-ol
synonyms:
- (7R,8S)-7-[(1S,2S)-1-carboxy-2-methylbutyl]amino-2-([(1S,2R)-1-amino-1-carboxypropan-2-yl]oxy)carbonyl-8-hydroxy-4-[(1S)-1-hydroxyethyl]-7,8-dihydroquinoline
identifiers:
- ns: mod
id: MOD:01395
- ns: pdb.ligand
id: QUA
- ns: resid
id: AA0472
structure: CC[C@@H]([C@@H](C(=O)O)N[C@@H]1C=Cc2c([C@H]1O)nc(cc2[C@@H](O)C)C(=O)O[C@@H]([C@@H](C=O)[NH3+])C)C
base_monomers:
- I
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
AA0618:
id: AA0618
name: O3-(poly-3-hydroxybutyrate)-L-serine
comments: The mechanism for transfer of the polymer from the synthase is uncertain.
The modification with two polymeric units is presented.
synonyms:
- O3-poly(3-hydroxybutyrate)serine
- O3-poly(3-hydroxybutanoic acid)serine
- O3-poly(beta-hydroxybutyrate)serine
- (2S)-2-amino-3-[([(3R)-3-hydroxybutanoyl]oxy)-poly([(3R)-3-methyl-1-oxopropane-1,3-diyl]oxy)]propanoic
acid
- O3-poly[(R)-3-hydroxybutyrate]serine
- O3-poly(3-hydroxybutanoate)serine
- O3-poly(3-hydroxybutyric acid)serine
identifiers:
- ns: cas
id: 29435-48-1
- ns: resid
id: AA0618
- ns: mod
id: MOD:01976
structure: C[C@H](CC(=O)O[C@@H](CC(=O)OC[C@@H](C(=O)O)[NH3+])C)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
- molecule: Monomer
element: H
position: 19
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
C, K:
id: AA0245
name: L-lysine thiazole-4-carboxylic acid
comments: Lysine is now thought not to be encoded in the peptide sequence modified
to produce GE2270. See RESID:AA0470.
synonyms:
- 2-[(1S)-1,5-diaminopentyl]-1,3-thiazole-4-carboxylic acid
- 2-[1,5-bis(azanyl)pentyl]-1,3-thiazole-4-carboxylic acid
identifiers:
- ns: mod
id: MOD:00250
- ns: go
id: GO:0018141
- ns: resid
id: AA0245
structure: OC(=O)c1csc(n1)[C@@H]([NH3+])CCCC[NH3+]
base_monomers:
- K
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
AA0092:
id: AA0092
name: L-lysine amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- lysinamide
- 6-ammonio-L-norleucinamide
- (2S)-2,6-diaminohexanamide
- '[(5S)-5,6-diamino-6-oxo-hexyl]azanium'
- K
- 2,6-diamino-hexanoic acid amide
identifiers:
- ns: resid
id: AA0092
- ns: cas
id: 32388-19-5
- ns: chebi
id: CHEBI:21353
- ns: pdb-ccd
id: LYN
- ns: go
id: GO:0018045
- ns: mod
id: MOD:00101
- ns: pdb.ligand
id: NH2
structure: '[NH3+]CCCC[C@@H](C(=O)N)[NH3+]'
base_monomers:
- K
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AA0036:
id: AA0036
name: 3'-phospho-L-histidine
comments: 'In the older biochemical literature this is usually called histidine-1-phosphate.
See also RESID:AA0035. The crystallographic designation for the substituted
nitrogen is delta-1, D1. Generating Enzyme: protein-histidine pros-kinase (EC
2.7.3.11).'
synonyms:
- nd1-phosphonohistidine
- (2S)-2-amino-3-(3-phosphonoimidazol-1-ium-4-yl)propanoic acid
- pros-phosphohistidine
- histidine-1-phosphate [misnomer]
- N3-phosphonohistidine
- 3-(1-phosphono-1H-imidazol-3-ium-5-yl)-L-alanine
- H
- ND1-phosphonohistidine
- N(pi)-phosphohistidine
- histidine-N(delta)-phosphate
- 2-azanyl-3-(3-phosphono-3H-imidazol-4-yl)propanoic acid
- histidine-N3'-phosphate
- (2S)-2-amino-3-(3-phosphono-3H-imidazol-4-yl)propanoic acid
identifiers:
- ns: pdb-ccd
id: HIP
- ns: pdb.ligand
id: HIP
- ns: mod
id: MOD:00045
- ns: resid
id: AA0036
- ns: cas
id: 5789-15-1
- ns: go
id: GO:0018106
structure: OC(=O)[C@H](Cc1cncn1P(=O)([O-])[O-])[NH3+]
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
AA0502:
id: AA0502
name: 5-glutamyl 2-aminoadipic acid
comments: 'Generating Enzyme: alpha-aminoadipate--LysW ligase, LysX (EC 6.3.2.-).'
synonyms:
- N2-(isoglutamyl)-2-aminoadipic acid
- (2S)-2-([(4S)-4-amino-4-carboxybutanoyl]amino)hexanedioic acid
- N2-(gamma-glutamyl)-2-aminoadipic acid
identifiers:
- ns: resid
id: AA0502
- ns: mod
id: MOD:01605
structure: O=C[C@H](CCC(=O)N[C@H](C(=O)[O-])CCCC(=O)[O-])[NH3+]
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
AA0086:
id: AA0086
name: L-glutamine amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- (2S)-2-aminopentanediamide
- glutaminamide
- L-glutamamide
- (2~{S})-2-azanylpentanediamide
- l-glutamamide
identifiers:
- ns: pdb-ccd
id: '6E4'
- ns: mod
id: MOD:00095
- ns: cas
id: 2013-17-4
- ns: chebi
id: CHEBI:21309
- ns: resid
id: AA0086
- ns: go
id: GO:0018039
- ns: pdb.ligand
id: NH2
structure: NC(=O)CC[C@@H](C(=O)N)[NH3+]
base_monomers:
- Q
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0351:
id: AA0351
name: S-(4a-FMN)-L-cysteine
comments: 'This modification forms as an intermediate in light transduction and
some redox reactions. The keyword "phosphoprotein" is not used with flavin modifications
linked through the flavin. Generating Enzyme: autocatalytic.'
synonyms:
- 4a-(S-cysteinyl)FMN
- (R)-2-amino-3-(4a-riboflavin 5'-dihydrogen phosphate)sulfanylpropanoic acid
- 4a-(S-cysteinyl)flavin mononucleotide
identifiers:
- ns: go
id: GO:0050742
- ns: resid
id: AA0351
- ns: pdb.ligand
id: FMN
- ns: mod
id: MOD:00356
structure: O=C1NC(=O)[C@]2(C(=N1)N(C[C@@H]([C@@H]([C@@H](COP(=O)([O-])[O-])O)O)O)c1c(N2)cc(c(c1)C)C)SC[C@@H](C(=O)O)N
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 39
l_bond_atoms:
- molecule: Monomer
element: N
position: 42
r_displaced_atoms:
- molecule: Monomer
element: O
position: 41
- molecule: Monomer
element: H
position: 41
l_displaced_atoms:
- molecule: Monomer
element: H
position: 42
AA0076:
id: AA0076
name: N6-methyl-L-lysine
comments: 'Generating Enzyme: histone-lysine N-methyltransferase (EC 2.1.1.43);
cytochrome-c-lysine N-methyltransferase (EC 2.1.1.59); calmodulin-lysine N-methyltransferase
(EC 2.1.1.60).'
synonyms:
- N~6~-methyl-L-lysine
- N(zeta)-methyllysine
- (2S)-2-amino-6-methylaminohexanoic acid
- K
- epsilon-methyllysine
- (2S)-2-amino-6-methylamino-hexanoic acid
- n-methyl-lysine
identifiers:
- ns: pdb.ligand
id: MLZ
- ns: cas
id: 1188-07-4
- ns: resid
id: AA0076
- ns: mod
id: MOD:00085
- ns: go
id: GO:0018024
- ns: chebi
id: CHEBI:61928
- ns: pdb-ccd
id: MLZ
structure: C[NH2+]CCCC[C@@H](C(=O)O)[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
AA0304:
id: AA0304
name: L-beta-carboxyaspartic acid
comments: This extremely acid labile modification has been detected but not located
by sequencing in proteins.
synonyms:
- 2-amino-3-carboxybutanedioic acid
- beta-carboxyaspartic acid
- (2S)-2-aminoethane-1,1,2-tricarboxylic acid
- 3-carboxyaspartic acid
identifiers:
- ns: resid
id: AA0304
- ns: mod
id: MOD:00309
- ns: go
id: GO:0019803
- ns: cas
id: 75898-26-9
structure: O=C[C@H](C(C(=O)[O-])C(=O)[O-])[NH3+]
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
AA0265:
id: AA0265
name: 1-thioglycine
comments: As a peptide this may exist predominantly in the iminyl-thiol [-C(SH)=N-]
tautomeric form. See also RESID:AA0206.
synonyms:
- 2-amino-1-sulfanylethanone
- 'aminoethanethioic O-acid #link INT'
- 'aminoethanethiolic acid #link CTER'
- 'aminoethanethionic acid #link INT'
- aminoethanethioic S-acid
- 'aminoethanethioic S-acid #link CTER'
- aminoethanethioic acid
- G
- thioglycin
- 2-aminoethanethioic S-acid
- aminothioacetic acid
identifiers:
- ns: cas
id: 758-10-1
- ns: pdb.ligand
id: GL3
- ns: pdb-ccd
id: GL3
- ns: go
id: GO:0018173
- ns: mod
id: MOD:00270
- ns: resid
id: AA0265
- ns: mod
id: MOD:01623
structure: C([NH3+])C=S
base_monomers:
- G
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
AA0601:
id: AA0601
name: (3R)-3-hydroxy-L-arginine
comments: 'The diastereomer (2S,3S)-3-hydroxyarginine is produced in non-ribosomal
antibiotic peptides of Streptomyces vinaceus. Generating Enzyme: ribosomal protein
L16 arginine hydroxylase ycfD (EC 1.14.11.-).'
synonyms:
- (2S,3R)-2-amino-5-[(diaminomethylidene)amino]-3-hydroxypentanoic acid
- 2-amino-5-[(aminoiminomethyl)amino]-3-hydroxypentanoic acid [tautomer]
- 2-amino-5-(carbamimidamido)-3-hydroxypentanoic acid [tautomer]
- C(beta)-hydroxyarginine
- beta-hydroxyarginine
- 2-amino-5-guanidino-3-hydroxypentanoic acid
identifiers:
- ns: resid
id: AA0601
- ns: mod
id: MOD:01956
structure: O[C@@H]([C@@H](C(=O)O)[NH3+])CC[NH+]=C(N)N
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
- molecule: Monomer
element: H
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
AA0372:
id: AA0372
name: 1'-(phospho-5'-uridine)-L-histidine
synonyms:
- tele-5'-uridylic-L-histidine
- (S)-2-amino-3-[1-(5'-uridine phosphono)imidazol-4-yl]propanoic acid
- L-histidine monoanhydride with 5'-uridylic acid
- N(tau)-5'-uridylic-L-histidine
- L-histidine 5'-uridine phosphoramidester
- N1'-uridylylated histidine
identifiers:
- ns: mod
id: MOD:00377
- ns: resid
id: AA0372
- ns: pdb.ligand
id: U5P
- ns: go
id: GO:0051110
structure: OC(=O)[C@@H](Cc1ncn(c1)[P@@](=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1ccc(=O)[nH]c1=O)[O-])[NH3+]
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 37
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 37
- molecule: Monomer
element: H
position: 37
charge: 1
AA0528:
id: AA0528
name: 5-glutamyl serotonin
comments: 'The structure shown in PubChem for this name is incorrect being instead
alpha-glutamyl serotonin, which is not the product of transamidation. Generating
Enzyme: protein-glutamine gamma-glutamyltransferase (EC 2.3.2.13).'
synonyms:
- (2S)-2-amino-5-([2-(5-hydroxy-1H-indol-3-yl)ethyl]amino)-5-oxopentanoic acid
- N2-(gamma-glutamyl)-5-hydoxytryptamine
- N5-[2-(5-hydroxy-3-indolyl)ethyl]glutamine
identifiers:
- ns: mod
id: MOD:01775
- ns: resid
id: AA0528
- ns: cas
id: 61059-62-9
structure: O=C(CC[C@@H](C(=O)O)[NH3+])NCCc1c[nH]c2c1cc(O)cc2
base_monomers:
- Q
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
AA0275:
id: AA0275
name: N-pyruvic acid 2-iminyl-L-valine
synonyms:
- (S)-2-(1-carboxy-2-methylpropanimino)propanoic acid
identifiers:
- ns: resid
id: AA0275
- ns: mod
id: MOD:00280
- ns: go
id: GO:0018388
structure: O=C[C@H](C(C)C)[NH2+][C@H](C(=O)[O-])C
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
AA0178:
id: AA0178
name: L-thyroxine
synonyms:
- O-(4-hydroxy-3,5-diiodophenyl)-3,5-diiodo-L-tyrosine
- (S)-2-amino-3-[4-(4-hydroxy-3,5-diiodophenoxy)-3,5-diiodophenyl]propanoic acid
- T4
- 3,3',5,5'-tetraiodo-L-thyronine
- 3,5,3',5'-tetraiodo-L-thyronine
- 3',3'',5',5''-tetraiodo-L-thyronine
- 4-(4-hydroxy-3,5-diiodophenoxy)-3,5-diiodo-L-phenylalanine
identifiers:
- ns: go
id: GO:0018078
- ns: cas
id: 51-48-9
- ns: resid
id: AA0178
- ns: chebi
id: CHEBI:18332
- ns: pdb.ligand
id: T44
- ns: mod
id: MOD:00187
structure: OC(=O)[C@H](Cc1cc(I)c(c(c1)I)Oc1cc(I)c(c(c1)I)O)[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 25
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 25
- molecule: Monomer
element: H
position: 25
charge: 1
C, R:
id: AA0553
name: 2-(4-guanidinobutanoyl)-5-hydroxy-imidazole-4-carbothionic
comments: The amino group of the following amino acid forms a thiopeptide bond.
This is an amino(sulfanyl)methylidene in the tautomeric form, which is shown
in the diagram and model.
synonyms:
- 2-(4-guanidinobutanoyl)-5-hydroxy-1H-imidazole-4-carbothioic O-acid
- (4Z)-2-(4-guanidinobutanoyl)-5-oxo-4-(sulfanylmethylidene)-4,5-dihydro-1H-imidazole
- 2-(4-guanidinobutanoyl)-5-hydroxy-4-thioformyl-1H-imidazole [tautomer]
identifiers:
- ns: mod
id: MOD:01877
- ns: resid
id: AA0553
structure: '[S-]/C=C/1\N=C(NC1=O)C(=O)CCC[NH+]=C(N)N'
base_monomers:
- R
- C
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
AA0620:
id: AA0620
name: N,N-dimethylglyine
comments: 'This modification is a minor post-translational modification in the
incomplete trimethylation of N-terminal glycine. See also RESID:AA0063 and RESID:AA0619.
This modification is readily formed artifactually from N-terminal glycine by
reductive methylation using formaldehyde. It is not clear whether "N-terminal
methyltransferase" defined in EC 2.1.1.244 is intended to exclude an enzyme
activity that methylates N-terminal glycine, or whether there are distinguishable
enzyme activities. Generating Enzyme: protein N-terminal methyltransferase (EC
2.1.1.244).'
synonyms:
- 1-carboxy-N,N-dimethylaminomethane
- (dimethylamino)ethanoic acid
- 2-(dimethylamino)acetic acid
- vitamin B16
identifiers:
- ns: cas
id: 1118-68-9
- ns: pdb.ligand
id: DMG
- ns: mod
id: MOD:01983
- ns: chebi
id: CHEBI:17724
- ns: resid
id: AA0620
structure: OC(=O)C[NH+](C)C
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
AA0253:
id: AA0253
name: S-(2-aminovinyl)-3-methyl-D-cysteine
comments: 'This cross-link arises from the decarboxylation of the carboxyl-terminal
portion of 3-methyllanthionine. Generating Enzyme: peptidyl-phosphoserine/phosphothreonine
dehydratase (EC 4.2.1.-); peptidyl-cysteine dehydroalanine/dehydrobutyrine ligase
(EC 6.2.-.-).'
synonyms:
- alpha-aminobutyric acid
- decarboxylated methyllanthionine
- (2S)-2-aminobutanoic acid
- (2S)-2-azanylbutanoic acid
- (2S,3S)-2-amino-3-[((Z)-2-aminoethenyl)sulfanyl]butanoic acid
- A
- 2-amino-3-[(2-aminovinyl)sulfanyl]butanoic acid
identifiers:
- ns: pdb-ccd
id: ABA
- ns: resid
id: AA0253
- ns: mod
id: MOD:00258
- ns: pdb.ligand
id: ABA
- ns: go
id: GO:0018162
structure: C[C@@H]([C@H]([NH3+])C(=O)O)S/C=C\N
base_monomers:
- T
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
AA0186:
id: AA0186
name: lactic acid
comments: 'The stereochemistry has not been determined in all the peptides with
this modification. Generating Enzyme: protein-serine dehydratase ElxB (EC 4.2.1.-);
D-lactoyl-protein dehydrogenase ElxO (EC 1.1.1.-).'
synonyms:
- 2-hydroxypropionic acid
- alpha-hydroxypropionic acid
- (2R)-2-hydroxypropanoic acid
identifiers:
- ns: resid
id: AA0186
- ns: pdb.ligand
id: LAC
- ns: cas
id: 10326-41-7
- ns: go
id: GO:0018084
- ns: chebi
id: CHEBI:42111
- ns: mod
id: MOD:00194
structure: OC(=O)[C@@H](O)C
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
AA0585:
id: AA0585
name: N6-phospho-L-lysine
comments: N6-phospho-L-lysine hydrolyzes rapidly at acidic pH, but is more stable
at neutral pH and below freezing. Although N6-phospho-L-lysine has been proposed
to occur in histone H1, its occurrence has not been reported in a sequenced
peptide.
synonyms:
- N(epsilon)-phosphoryllysine
- (2S)-2-amino-6-(phosphonoamino)hexanoic acid
- N(epsilon)-phospholysine
- N(epsilon)-phosphonolysine
- (2S)-2-azanyl-6-(phosphonoamino)hexanoic acid
- 6-phospholysine
- N(6)-phosphonolysine
- N(epsilon)-phosphonyllysine
identifiers:
- ns: cas
id: 14721-74-5
- ns: resid
id: AA0585
- ns: mod
id: MOD:01931
structure: '[NH3+][C@H](C(=O)O)CCCCNP(=O)([O-])[O-]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AA0110:
id: AA0110
name: L-lanthionine
comments: This diastereomeric form, which retains the conformation of the R chiral
center of L-cysteine, does occur naturally but is not common. See RESID:AA0111.
synonyms:
- (R,R)-2,6-diamino-4-thiaheptanedioic acid
- 3,3'-thiobis-L-alanine
- (R)-S-(2-amino-2-carboxyethyl)-L-cysteine
- (R,R)-3,3'-thiobis-(2-aminopropanoic acid)
- 2-amino-3-(2-amino-2-carboxyethyl)sulfanylpropanoic acid
- (R,R)-bis(2-amino-2-carboxyethyl)sulfide
- (2R,2'R)-3,3'-sulfanediylbis(2-aminopropanoic acid)
identifiers:
- ns: mod
id: MOD:01837
- ns: chebi
id: CHEBI:21347
- ns: go
id: GO:0018081
- ns: cas
id: 922-55-4
- ns: resid
id: AA0110
- ns: mod
id: MOD:00119
structure: O=C[C@H](CSC[C@@H](C(=O)O)[NH3+])[NH3+]
base_monomers:
- S
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
AA0315:
id: AA0315
name: 4-(S-L-cysteinyl)-L-glutamic acid
synonyms:
- (2S,4S)-2-amino-4-[(R)-2-amino-2-carboxyethyl]sulfanylpentanedioic acid
- (2S,3S,7R)-2,7-diamino-4-carboxy-5-thiaoctanedioic acid
identifiers:
- ns: go
id: GO:0019929
- ns: resid
id: AA0315
- ns: mod
id: MOD:00320
- ns: chebi
id: CHEBI:20293
structure: O=C[C@H](CS[C@H](C(=O)[O-])C[C@@H](C=O)[NH3+])[NH3+]
base_monomers:
- E
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
C, I:
id: AA0466
name: L-isoleucine thiazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-cysteine
cyclase (EC 4.2.1.-); peptidyl-thiazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-[1-zanyl-2-methylbutyl]-1,3-thiazole-4-carboxylic acid
- 2-[(1S,2S)-1-amino-2-methylbutyl]-1,3-thiazole-4-carboxylic acid
identifiers:
- ns: mod
id: MOD:01389
- ns: pdb.ligand
id: BB9
- ns: resid
id: AA0466
structure: C[C@H]([C@H]([NH3+])c1nc(cs1)C(=O)O)CC
base_monomers:
- I
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
- molecule: Monomer
element: H
position: 17
AA0111:
id: AA0111
name: meso-lanthionine
comments: 'This diastereomeric form, despite the appearance of the same stereochemical
designator, inverts the conformation of the S chiral center of L-serine to a
D-alanine skeleton with S chiralty because of the altered prority of the beta-carbon.
The stereosymmetry of the meso-form is broken within a peptide chain. Generating
Enzyme: peptidyl-phosphoserine/phosphothreonine dehydratase (EC 4.2.1.-); peptidyl-cysteine
dehydroalanine/dehydrobutyrine ligase (EC 6.2.-.-).'
synonyms:
- (2S,6R)-meso-lanthionine [misnomer]
- (R)-S-(2-amino-2-carboxyethyl)-D-cysteine
- (2S)-2-amino-3-[[(2R)-2-amino-2-carboxyethyl]sulfanyl]propanoic acid
- (R,S)-bis(2-amino-2-carboxyethyl)sulfide
- (2R,2'S)-3,3'-sulfanediylbis(2-aminopropanoic acid)
- (2R,2'S)-3,3'-thiobis-(2-aminopropanoic acid)
- (2R,6S)-meso-lanthionine
- (2R,6S)-2,6-diamino-4-thiaheptanedioic acid
- 3,3'-thiobis-meso-alanine
- cysteine-3-D-alanine thioether
identifiers:
- ns: pdb.ligand
id: DAL
- ns: cas
id: 922-56-5
- ns: mod
id: MOD:00120
- ns: go
id: GO:0018081
- ns: resid
id: AA0111
- ns: chebi
id: CHEBI:25013
structure: O=C[C@H](CSC[C@H](C(=O)O)[NH3+])[NH3+]
base_monomers:
- S
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
AA0072:
id: AA0072
name: L-glutamic acid 5-methyl ester
comments: 'Glutamate methylesterase can also act as a glutamine amidohydrolase.
Generating Enzyme: protein-glutamate O-methyltransferase (EC 2.1.1.80).'
synonyms:
- (2S)-2-amino-5-methoxy-5-oxopentanoic acid
- 5-methyl L-glutamate
- (5)-methyl L-hydrogen glutamate
- 5-methyl L-2-aminoglutarate
- glutamic acid 5-methyl ester
- glutamic acid gamma-methyl ester
- 2-aminopentanedioic acid 5-methyl ester
identifiers:
- ns: go
id: GO:0008983
- ns: mod
id: MOD:00657
- ns: cas
id: 1499-55-4
- ns: resid
id: AA0072
- ns: go
id: GO:0018390
- ns: mod
id: MOD:00081
structure: COC(=O)CC[C@@H](C(=O)O)[NH3+]
base_monomers:
- E
- Q
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
- molecule: Monomer
element: H
position: 11
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
AA0404:
id: AA0404
name: O-fucosyl-L-serine
comments: 'See also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291,
RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402,
RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines. Generating
Enzyme: peptide-O-fucosyltransferase (EC 2.4.1.221).'
synonyms:
- O3-fucosylserine
- (2S)-2-amino-3-(6-deoxy-alpha-D-galactopyranosyloxy)propanoic acid
- O-glycosylserine
identifiers:
- ns: resid
id: AA0404
- ns: mod
id: MOD:00812
structure: OC(=O)[C@H](CO[C@H]1O[C@H](C)[C@@H]([C@@H]([C@H]1O)O)O)[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 23
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 23
- molecule: Monomer
element: H
position: 23
charge: 1
AA0232:
id: AA0232
name: L-beta-methylthioaspartic acid
comments: 'The stereochemistry for the second chiral center has not been resolved.
The (2R,3S) form is shown. beta-Methylthioaspartic acid probably occurs uniquely
in ribosomal protein S12. Althouh the aspartic acid is invariant, the modification
is not required for activity. Generating Enzyme: ribosomal protein S12 methylthiotransferase
RimO (EC 2.-.-.-).'
synonyms:
- 3-methylthio-aspartic acid
- 3-carboxy-S-methyl-cysteine
- beta-methylthio-aspartic acid
- (2R,3Xi)-2-amino-3-(methylsulfanyl)butanedioic acid
identifiers:
- ns: cas
id: 180420-54-6
- ns: go
id: GO:0018339
- ns: resid
id: AA0232
- ns: mod
id: MOD:00237
structure: CS[C@@H]([C@@H](C=O)[NH3+])C(=O)[O-]
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
AA0071:
id: AA0071
name: N5-methyl-L-glutamine
synonyms:
- gamma-methylglutamine
- (2S)-2-amino-5-methylamino-5-oxo-pentanoic acid
- N-methylglutamine
- N-methyl-L-glutamine
- (2S)-2-amino-5-methylamino-5-oxopentanoic acid
- N(delta)-methylglutamine
- n5-methylglutamine
- 2-amino-N5-methylpentanediamic acid
- Q
identifiers:
- ns: pdb.ligand
id: MEQ
- ns: pdb-ccd
id: MEQ
- ns: go
id: GO:0018019
- ns: resid
id: AA0071
- ns: cas
id: 3031-62-7
- ns: chebi
id: CHEBI:61891
- ns: mod
id: MOD:00080
structure: CNC(=O)CC[C@@H](C(=O)O)[NH3+]
base_monomers:
- Q
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
- molecule: Monomer
element: H
position: 11
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
AA0303:
id: AA0303
name: L-glutamimide
comments: This modification is autocatalytically produced from the carboxyl-terminal
glutamine of spliced inteins.
synonyms:
- 2-aminopentanimide
- alpha-aminoglutarimide
- 3-amino-2,6-piperidinedione
- (3S)-3-aminopiperidine-2,6-dione
identifiers:
- ns: cas
id: 2353-44-8
- ns: go
id: GO:0019802
- ns: resid
id: AA0303
- ns: mod
id: MOD:00308
structure: N[C@H]1CCC(=O)NC1=O
base_monomers:
- Q
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0504:
id: AA0504
name: 5-glutamyl allysine
synonyms:
- alpha-(gamma-glutamyl)allysine
- 2-(5-glutamyl)amino-6-oxohexanoic acid
- (2S)-2-([(4S)-4-amino-4-carboxybutanoyl]amino)-6-oxohexanoic acid
- N2-(isoglutamyl)allysine
- N2-(gamma-glutamyl)allysine
identifiers:
- ns: resid
id: AA0504
- ns: mod
id: MOD:01607
structure: O=CCCC[C@@H](C(=O)[O-])NC(=O)CC[C@@H](C=O)[NH3+]
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
AA0322:
id: AA0322
name: 3-hydroxy-L-tryptophan
synonyms:
- (2S,3S)-2-amino-3-hydroxy-3-(1H-indol-3-yl)propanoic acid
- (betaS)-beta-hydroxy-L-tryptophan
- beta-hydroxytryptophane
- W
- 3-hydroxytryptophan
- beta-hydroxytryptophan
identifiers:
- ns: pdb-ccd
id: HTR
- ns: go
id: GO:0045325
- ns: mod
id: MOD:00327
- ns: pdb.ligand
id: HTR
- ns: resid
id: AA0322
structure: OC(=O)[C@H]([C@H](c1c[nH]c2c1cccc2)O)N
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
AA0089:
id: AA0089
name: L-histidine amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- histidinamide
- (2S)-2-amino-3-(1H-imidazol-4-yl)propanamide
- H
- L-histidinamide
- (2S)-2-amino-3-(3H-imidazol-4-yl)propanamide
- l-histidine amide
identifiers:
- ns: pdb.ligand
id: HIA
- ns: chebi
id: CHEBI:43042
- ns: mod
id: MOD:00098
- ns: resid
id: AA0089
- ns: pdb-ccd
id: HIA
- ns: go
id: GO:0018042
- ns: cas
id: 7621-14-9
structure: NC(=O)[C@@H]([NH3+])Cc1cnc[nH]1
base_monomers:
- H
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0363:
id: AA0363
name: N-carboxy-L-methionine
comments: At least three protein crystallographic structures have been reported
with this modification. However, no chemical evidence for this modification
is provided, there were no reports of this modification before these crystallographic
reports, and there is no metabolic explanation for the conversion of a formyl
group to a carboxy group. There is confusion in its description, and misnaming
is common. This modification is probably a misidentification of N-(dihydroxymethyl)methionine,
the hydrated form of N-formylmethionine. See RESID:AA0493.
synonyms:
- N-carboxy-L-methionine
- (2S)-2-(carboxyamino)-4-methylsulfanyl-butanoic acid
- (S)-2-carboxyamino-4-(methylsulfanyl)butanoic acid
- n-carboxymethionine
- N-carboxymethionine
- M
- 2-carbamic-4-(methylsulfanyl)butanoic acid
- 2-carbamic-4-(methylthio)butanoic acid
identifiers:
- ns: pdb.ligand
id: CXM
- ns: mod
id: MOD:00368
- ns: go
id: GO:0050988
- ns: pdb-ccd
id: CXM
- ns: resid
id: AA0363
- ns: chebi
id: CHEBI:61924
structure: '[O-]C(=O)N[C@H](C(=O)O)CCSC'
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
AA0063:
id: AA0063
name: N-methylglycine
comments: 'Sarcosine occurs internally in some nonencoded peptides. It has been
observed as a minor post-translational modification arising from the incomplete
trimethylation of N-terminal glycine. See RESID:AA0619 and RESID:AA0620. Polypeptides
with monomethylated amino terminals can undergo premature cleavage during the
coupling step of an Edman degradation. This can result in "preview" with both
a residue and the following residue being seen from the first step on through
a sequence. It is not clear whether "N-terminal methyltransferase" defined in
EC 2.1.1.244 is intended to exclude an enzyme activity that methylates N-terminal
glycine, or whether there are distinguishable enzyme activities. Generating
Enzyme: protein N-terminal methyltransferase (EC 2.1.1.244).'
synonyms:
- L-sarcosine
- methylaminoethanoic acid
- methylaminoacetic acid
identifiers:
- ns: pdb.ligand
id: SAR
- ns: mod
id: MOD:00072
- ns: resid
id: AA0063
- ns: cas
id: 107-97-1
- ns: go
id: GO:0018013
- ns: chebi
id: CHEBI:15611
structure: C[NH2+]CC(=O)O
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
- molecule: Monomer
element: H
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
AA0519:
id: AA0519
name: O-(ADP-ribosyl)-L-threonine
comments: 'It is not known whether Photorhabdus luminescens toxin catalyzes formation
of the alpha or beta isomer. The alpha form is presented. The keyword "phosphoprotein"
is not used with toxin modification. Generating Enzyme: NAD(P)+--threonine ADP-ribosyltransferase
TccC3 (EC 2.4.2.-).'
synonyms:
- (S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-butanoic
acid
- O3-alpha-D-ribofuranosyl-L-threonine 5'->5'-ester with adenosine 5'-(trihydrogen
diphosphate)
- O3-(ADP-ribosyl)-L-threonine
- O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-threonine
identifiers:
- ns: resid
id: AA0519
- ns: mod
id: MOD:01663
structure: OC(=O)[C@H]([C@H](O[C@H]1O[C@H]([C@H]([C@H]1O)O)CO[P@@](=O)(O[P@](=O)(OC[C@@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1NC=N[C@H]2N)[O-])[O-])C)[NH3+]
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 54
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 54
- molecule: Monomer
element: H
position: 54
charge: 1
AA0311:
id: AA0311
name: N4,N4-dimethyl-L-asparagine
comments: This structure has not been confirmed.
synonyms:
- (2S)-2-amino-4-dimethylamino-4-oxo-butanoic acid
- beta-dimethylasparagine [misnomer]
- N,N-dimethyl-L-asparagine
- N(gamma),N(gamma)-dimethylasparagine
- 2-amino-N4,N4-dimethylbutanediamic acid
- n4,n4-dimethyl-asparagine
- (2S)-2-amino-4-(dimethylamino)-4-oxobutanoic acid
- N
identifiers:
- ns: mod
id: MOD:00316
- ns: pdb-ccd
id: DMH
- ns: resid
id: AA0311
- ns: pdb.ligand
id: DMH
- ns: go
id: GO:0019710
structure: N[C@H](C(=O)O)CC(=O)N(C)C
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AA0316:
id: AA0316
name: cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid L-aspartate ester
comments: The stereochemistry for the second chiral center has not been resolved.
The (14S) form is shown.
synonyms:
- (7Z,14Xi)-14-[(S)-3-amino-3-carboxy-propanoyl]oxy-10,13-dioxo-7-heptadecenoic
acid
- barley lipid transfer protein modification
identifiers:
- ns: mod
id: MOD:00321
- ns: go
id: GO:0019930
- ns: resid
id: AA0316
structure: CCC[C@@H](C(=O)CCC(=O)C/C=C\CCCCCC(=O)[O-])OC(=O)C[C@@H](C=O)[NH3+]
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 31
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 31
- molecule: Monomer
element: H
position: 31
charge: 1
AA0042:
id: AA0042
name: N-acetyl-L-aspartic acid
comments: 'Generating Enzyme: aspartate N-acetyltransferase (EC 2.3.1.17).'
synonyms:
- 2-(acetylamino)butanedioic acid
- 2-(acetylazanyl)butanedioic acid
- acetylaspartic acid
- (2S)-2-(acetamido)butanedioic acid
identifiers:
- ns: cas
id: 997-55-7
- ns: go
id: GO:0017190
- ns: mod
id: MOD:00051
- ns: chebi
id: CHEBI:21547
- ns: resid
id: AA0042
structure: O=C[C@@H](NC(=O)C)CC(=O)[O-]
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
AA0156:
id: AA0156
name: 1'-mannosyl-L-tryptophan
comments: In 1992, the hexose was not identified and it was proposed, but not
established, that this modification had an N-linked glycosidic bond. After C-linked
2'-mannosyltryptophan was found in vertebrate proteins, it was generally assumed
that the tryptophan N-glycoside structure was wrong. See RESID:AA0217 for 2'-mannosyltryptophan.
The alpha anomeric form is shown.
synonyms:
- (2S)-2-amino-3-(1-D-mannopyranosyloxy-1H-indol-3-yl)propanoic acid
- N-mannosyl-tryptophan
- 1'-glycosyl-L-tryptophan
- N1-mannosyl-tryptophan
identifiers:
- ns: resid
id: AA0156
- ns: mod
id: MOD:00165
- ns: go
id: GO:0006487
structure: OC[C@H]1O[C@@H]([C@H]([C@H]([C@@H]1O)O)O)n1cc(c2c1cccc2)C[C@@H](C(=O)O)[NH3+]
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 29
l_bond_atoms:
- molecule: Monomer
element: N
position: 32
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 31
- molecule: Monomer
element: H
position: 31
l_displaced_atoms:
- molecule: Monomer
element: H
position: 32
- molecule: Monomer
element: H
position: 32
charge: 1
AA0364:
id: AA0364
name: O-acetyl-L-serine
synonyms:
- serine acetate ester
- o-acetylserine
- (2S)-3-acetyloxy-2-amino-propanoic acid
- O-acetyl-L-serine
- (2S)-3-(acetyloxy)-2-aminopropanoic acid
- O-acetylserine
- S
identifiers:
- ns: mod
id: MOD:00369
- ns: go
id: GO:0030919
- ns: pdb-ccd
id: OAS
- ns: cas
id: 4985-36-8
- ns: resid
id: AA0364
- ns: pdb.ligand
id: OAS
- ns: chebi
id: CHEBI:17981
structure: CC(=O)OC[C@@H](C(=O)O)[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
AA0091:
id: AA0091
name: L-leucine amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- L-leucinamide
- 2-azanyl-4-methylpentanamide
- 2-amino-4-methylvaleramide
- alpha-aminoisocaproamide
- l-leucinamide
- (2S)-2-amino-4-methylpentanamide
- (2~{S})-2-azanyl-4-methyl-pentanamide
- L
- leucinamide
identifiers:
- ns: chebi
id: CHEBI:21349
- ns: mod
id: MOD:00100
- ns: cas
id: 687-51-4
- ns: resid
id: AA0091
- ns: pdb-ccd
id: NLW
- ns: pdb.ligand
id: NH2
- ns: go
id: GO:0018044
structure: '[NH3+][C@H](C(=O)N)CC(C)C'
base_monomers:
- L
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AA0065:
id: AA0065
name: N-methyl-L-phenylalanine
comments: 'Polypeptides with monomethylated amino terminals can undergo premature
cleavage during the coupling step of an Edman degradation. This can result in
"preview" with both a residue and the following residue being seen from the
first step on through a sequence. Generating Enzyme: prepilin peptidase (EC
3.4.23.43).'
synonyms:
- N-methylphenylalanine
- (2S)-2-methylamino-3-phenylpropanoic acid
- (2S)-2-(methylamino)-3-phenyl-propanoic acid
- F
- n-methylphenylalanine
- N-methyl-L-phenylalanine
identifiers:
- ns: chebi
id: CHEBI:61884
- ns: resid
id: AA0065
- ns: pdb.ligand
id: MEA
- ns: go
id: GO:0018015
- ns: pdb-ccd
id: MEA
- ns: cas
id: 2566-30-5
- ns: mod
id: MOD:00074
structure: OC(=O)[C@H](Cc1ccccc1)[NH2+]C
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
AA0144:
id: AA0144
name: 3'-(8alpha-FAD)-L-histidine
comments: 'The arrangement of the attachment has not been completely established
in some cases. The keyword "phosphoprotein" is not used with flavin modifications
linked through the flavin. Generating Enzyme: autocatalytic.'
synonyms:
- 8alpha-N1-histidyl FAD [misnomer]
- pros-(8alpha-FAD)-histidine
- 8alpha-(N(delta)-histidyl)FAD
- N(pi)-(8alpha-FAD)-histidine
- 8alpha-(N3'-histidyl)FAD
- (2S)-2-amino-3-(3-[8alpha-riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester
with adenosine]imidazol-4-yl)propanoic acid
identifiers:
- ns: mod
id: MOD:00153
- ns: pdb.ligand
id: FAD
- ns: resid
id: AA0144
- ns: go
id: GO:0018295
structure: O=C1[N-]C(=O)C2C(N1)N(C[C@@H]([C@@H]([C@@H](CO[P@](=O)(O[P@@](=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc3c1ncnc3N)[O-])[O-])O)O)O)C1C(N2)CC(C(C1)Cn1cncc1C[C@@H](C(=O)O)[NH3+])C
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 68
l_bond_atoms:
- molecule: Monomer
element: N
position: 71
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 70
- molecule: Monomer
element: H
position: 70
l_displaced_atoms:
- molecule: Monomer
element: H
position: 71
- molecule: Monomer
element: H
position: 71
charge: 1
AA0277:
id: AA0277
name: S-selenyl-L-cysteine
synonyms:
- 2-amino-3-hydroselenosulfidopropanoic acid
- 2-amino-3-hydroselenylsulfidopropanoic acid
- 2-amino-3-hydroselenylthiopropanoic acid
- S-selanylcysteine
- S-selanyl-L-cysteine
- C
- cysteine perselenide [misnomer]
- (2R)-2-amino-3-selanylsulfanyl-propanoic acid
- (R)-2-amino-3-(selanylsulfanyl)propanoic acid
- S-selenylcysteine
- s-selanyl cysteine
identifiers:
- ns: resid
id: AA0277
- ns: go
id: GO:0018183
- ns: pdb.ligand
id: CSZ
- ns: pdb-ccd
id: CSZ
- ns: mod
id: MOD:00282
structure: OC(=O)[C@@H]([NH3+])CS[SeH]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
AA0624:
id: AA0624
name: 2-(L-cystein-S-yl)-D-serine
synonyms:
- (2S)-2-amino-2-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-3-hydroxypropanoic acid
- (2R,5S)-2,5-diamino-5-carboxy-6-hydroxy-4-thiahexanoic acid
identifiers:
- ns: pdb.ligand
id: DSN
- ns: mod
id: MOD:01987
- ns: resid
id: AA0624
structure: O=C[C@H](CS[C@](C(=O)O)(CO)N)[NH3+]
base_monomers:
- S
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
AA0616:
id: AA0616
name: S-methyl-L-methionine
comments: 'Generating Enzyme: autocatalytic.'
synonyms:
- S-methylmethioninium
- (3S)-(3-amino-3-carboxypropyl)dimethylsulfanium
- vitamin U
- S-methylmethionine
- '[(3S)-3-amino-3-carboxypropyl](dimethyl)sulfonium'
- (2S)-2-amino-4-(dimethylsulfonio)butanoate
identifiers:
- ns: cas
id: 4727-40-6
- ns: chebi
id: CHEBI:17728
- ns: mod
id: MOD:01974
- ns: resid
id: AA0616
structure: '[NH3+][C@H](C(=O)O)CC[S](C)C'
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AA0132:
id: AA0132
name: S-phycoerythrobilin-L-cysteine
comments: See the comment for S-phycocyanobilin-L-cysteine (RESID:AA0131). There
is an additional chiral center at C-16. The phytochromobilins and phycoerythrobilins
transmit red.
synonyms:
- PEB
- 18-ethenyl-3-[1-((2-amino-2-carboxy)ethylsulfanyl)ethyl]-2,3,15,16-tetrahydro-2,7,13,17-tetramethyl-1,19-dioxo-(21H,22H,24H)-bilin-8,12-dipropanoic
acid
- phycoerythrobilin cysteine adduct
- (2S,3R,16R)-18-ethenyl-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-2,3,15,16-tetrahydrobilin-1,19(21H,22H,24H)-dione
identifiers:
- ns: resid
id: AA0132
- ns: pdb.ligand
id: PEB
- ns: go
id: GO:0017011
- ns: mod
id: MOD:00141
- ns: chebi
id: CHEBI:15618
- ns: cas
id: 18097-67-1
structure: O=C[C@H](CS[C@@H]([C@H]1/C(=C/[C@@H]2[NH2+]/C(=C\c3[nH]c(c(c3CCC(=O)[O-])C)C[C@H]3NC(=O)C(=C3C)C=C)/C(=C2C)CCC(=O)[O-])/NC(=O)[C@H]1C)C)[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 28
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
AA0046:
id: AA0046
name: N-acetylglycine
synonyms:
- aceturic acid
- (acetylazanyl)ethanoic acid
- 2-(acetylamino)ethanoic acid
- 2-(acetamido)ethanoic acid
- (acetylamino)acetic acid
identifiers:
- ns: mod
id: MOD:00055
- ns: resid
id: AA0046
- ns: cas
id: 543-24-8
- ns: go
id: GO:0017193
- ns: chebi
id: CHEBI:61888
structure: CC(=O)NCC(=O)O
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
- molecule: Monomer
element: H
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
AA0179:
id: AA0179
name: 6'-bromo-L-tryptophan
synonyms:
- 6-bromo-L-tryptophan
- 6-bromo-tryptophan
- (2S)-2-amino-3-(6-bromo-1H-indol-3-yl)propanoic acid
- W
identifiers:
- ns: cas
id: 52448-17-6
- ns: pdb.ligand
id: BTR
- ns: chebi
id: CHEBI:61899
- ns: go
id: GO:0018080
- ns: mod
id: MOD:00188
- ns: pdb-ccd
id: BTR
- ns: resid
id: AA0179
structure: OC(=O)[C@H](Cc1c[nH]c2c1ccc(c2)Br)[NH3+]
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0182:
id: AA0182
name: (Z)-dehydrobutyrine
comments: 'In some cases it has not been firmly established whether the natural
form is the Z or the E isomer. For the E isomer, see RESID:AA0547. A 2,3-didehydro
amino acid blocks Edman degradation. Generating Enzyme: protein-threonine dehydratase
(EC 4.2.1.-); phosphothreonine lyase (EC 4.3.2.-).'
synonyms:
- 2,3-didehydrobutyrine
- 3-methyldehydroalanine
- (2Z)-2-aminobut-2-enoic acid
- anhydrothreonine
- (Z)-2-aminobutenoic acid
- Dhb
- (Z)-2-amino-2-butenoic acid
- methyl-dehydroalanine
- alpha,beta-dehydroaminobutyric acid
identifiers:
- ns: pdb.ligand
id: DBU
- ns: mod
id: MOD:00190
- ns: go
id: GO:0018082
- ns: cas
id: 71018-10-5
- ns: resid
id: AA0182
structure: C/C=C(/C(=O)O)\N
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
AA0222:
id: AA0222
name: omega-N-phospho-L-arginine
comments: 'Generating Enzyme: histone-arginine kinase (EC 2.7.3.-); protein-arginine
kinase (EC 2.7.3.-).'
synonyms:
- phosphoarginine
- N5-[imino(phosphonoamino)methyl]-L-ornithine
- (2S)-2-amino-5-([amino(phosphonoamino)methylidene]amino)pentanoic acid
- (2S)-2-amino-5-(N'-phosphonocarbamimidamido)pentanoic acid
- N(omega)-phosphono-L-arginine
- alpha-amino-delta-phosphonoguanidinovaleric acid
- N(gamma)-phosphoarginine
identifiers:
- ns: mod
id: MOD:00227
- ns: go
id: GO:0018109
- ns: cas
id: 1189-11-3
- ns: resid
id: AA0222
structure: OC(=O)[C@H](CCC/[NH+]=C(\NP(=O)([O-])[O-])/N)[NH3+]
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0196:
id: AA0196
name: D-asparagine
comments: 'Generating Enzyme: protein-asparagine epimerase (EC 5.1.1.-).'
synonyms:
- D-aspartic acid beta-amide
- (R)-2-amino-4-butanediamic acid
- D-alpha-aminosuccinamic acid
identifiers:
- ns: pdb.ligand
id: DSG
- ns: resid
id: AA0196
- ns: cas
id: 2058-58-4
- ns: mod
id: MOD:00203
- ns: go
id: GO:0018091
- ns: chebi
id: CHEBI:29957
structure: NC(=O)C[C@H](C(=O)O)N
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
AA0131:
id: AA0131
name: S-phycocyanobilin-L-cysteine
comments: 'A second linkage, an ester between a serine and one of the propanoic
acid groups, was reported at one time but was not confirmed. A second cysteine
linkage has also been reported to a moiety thought to be phycocyanobilin. The
phycocyanobilins transmit blue. Generating Enzyme: phycocyanobilin lyase (EC
4.4.1.-).'
synonyms:
- PCB
- phycobilin cysteine
- (2R,3R)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-18-ethyl-1,2,3,19,21,22,24-heptahydro-2,7,13,17-tetramethyl-1,19-dioxo-(21H,22H,24H)-bilin-8,12-dipropanoic
acid
- phycocyanobilin cysteine adduct
- (2R,3R)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-18-ethyl-2,7,13,17-tetramethyl-1,2,3,19,21,22,24-heptahydrobilin-1,19(21H,22H,24H)-dione
identifiers:
- ns: cas
id: 20298-86-6
- ns: chebi
id: CHEBI:15617
- ns: mod
id: MOD:00140
- ns: pdb.ligand
id: CYC
- ns: go
id: GO:0017009
- ns: resid
id: AA0131
structure: O=C[C@H](CS[C@@H]([C@H]1/C(=C/C2=C(C)[C@@H](/C(=C/c3[nH]c(c(c3CCC(=O)[O-])C)/C=C/3\NC(=O)C(=C3C)CC)/[NH2+]2)CCC(=O)[O-])/NC(=O)[C@H]1C)C)[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 28
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
r_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
AA0570:
id: AA0570
name: L-arginine thiazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-cysteine
cyclase (EC 4.2.1.-); peptidyl-thiazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-[(1S)-1-amino-4-([diaminomethylidene]amino)butyl]-1,3-thiazole-4-carboxylic
acid
identifiers:
- ns: resid
id: AA0570
- ns: mod
id: MOD:01899
structure: OC(=O)c1csc(n1)[C@H](CCC[NH+]=C(N)N)[NH3+]
base_monomers:
- R
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
AA0507:
id: AA0507
name: L-threonine methyl ester
synonyms:
- methyl (2S,3R)-2-amino-3-hydroxybutanoate
- methyl L-threoninate
identifiers:
- ns: resid
id: AA0507
- ns: cas
id: 3373-59-9
- ns: go
id: GO:0044608
- ns: mod
id: MOD:01610
structure: COC(=O)[C@H]([C@H](O)C)N
base_monomers:
- T
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
AA0241:
id: AA0241
name: glycine thiazole-4-carboxylic acid
comments: 'Formed by the condensation of a cysteine thiol with the carbonyl of
the preceding residue and alpha-beta dehydrogenation. Generating Enzyme: peptidyl-cysteine
cyclase (EC 4.2.1.-); peptidyl-thiazoline dehydrogenase (EC 1.3.-.-).'
synonyms:
- 2-(azanylmethyl)-1,3-thiazole-4-carboxylic acid
- 2-(aminomethyl)-1,3-thiazole-4-carboxylic acid
identifiers:
- ns: resid
id: AA0241
- ns: pdb.ligand
id: BB9
- ns: chebi
id: CHEBI:21276
- ns: cas
id: 25438-22-6
- ns: mod
id: MOD:00246
- ns: go
id: GO:0018137
structure: '[NH3+]Cc1scc(n1)C(=O)O'
base_monomers:
- C
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
AA0492:
id: AA0492
name: 3,3-dihydroxy-L-alanine
comments: 'This active site residue is formed by the spontaneous hydration of
the aldehyde, 2-amino-3oxopropanoic acid. See RESID:AA0185. The PDB hetgroup
FGL was originally designated as the "C(alpha)-formyl glycine" active site residue
L-3-oxoalanine observed in its hydrated form. That structure, a gem-diol with
an sp(3) carbon, was misinterpreted as a carboxyl with an sp(2) carbon, and
assigned to aminomalonic acid (see RESID:AA0458) instead. The hetgroup DDZ is
being introduced for 3,3-dihydroxyalanine. Generating Enzyme: sulfatase maturing
enzyme (sulfatase modifying factor, C-alpha-formylglycine-generating enzyme)
(EC 1.1.99.-) #link SER; sulfatase maturing enzyme (sulfatase modifying factor,
C-alpha-formylglycine-generating enzyme) (EC 1.8.99.-) #link CYS.'
synonyms:
- (S)-2-amino-3,3-dihydroxypropanoic acid
- 3,3-dihydroxy l-alanine
- (2S)-2-amino-3,3-dihydroxy-propanoic acid
- 2-(dihydroxymethyl)glycine
- 3-hydroxy-L-serine
- 3-oxoalanine hydrate
- A
- C(alpha)-formylglycine hydrate [misnomer]
- 3,3-dihydroxyalanine
identifiers:
- ns: pdb.ligand
id: DDZ
- ns: mod
id: MOD:01445
- ns: mod
id: MOD:01444
- ns: resid
id: AA0492
- ns: pdb-ccd
id: DDZ
structure: OC([C@@H](C(=O)O)N)O
base_monomers:
- A
- S
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
- molecule: Monomer
element: H
position: 7
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
AA0151:
id: AA0151
name: N4-(N-acetylamino)glucosyl-L-asparagine
comments: 'This modification typically occurs in extracellar peptides with an
NX[ST] motif. Partial modification has been observed to occur with cysteine,
rather than serine or threonine, in the third position. Secondary structure
features are important, and proline in the second or fourth positions inhibits
modification. See also RESID:AA0420 and RESID:AA0421 for other N4-glycosylated
asparagines. The PDB has some entries with asparagine apparently alpha-glycosylated
with N-acetylglucosamine, those with PDBHET:NDG. These are low resolution structures
and appear to be erroneous. Generating Enzyme: dolichyl-diphosphooligosaccharide-protein
glycotransferase (EC 2.4.1.119); protein N-acetylglucosaminyltransferase (EC
2.4.1.94).'
synonyms:
- N4-(N-acetylglucosaminyl)asparagine
- N4-glycosylasparagine
- N4-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-L-asparagine
- N4-(2-acetylamino-2-deoxy-beta-D-glucopyranosyl)-L-asparagine
- N4-glycosyl-L-asparagine
- (2S)-2-amino-4-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)amino-4-oxobutanoic
acid
- N4-asparagine-beta-N-acetylglucosaminide
identifiers:
- ns: go
id: GO:0006487
- ns: mod
id: MOD:00831
- ns: chebi
id: CHEBI:17261
- ns: cas
id: 10036-64-3
- ns: pdb.ligand
id: NAG
- ns: resid
id: AA0151
structure: OC[C@H]1O[C@@H](NC(=O)C[C@@H](C(=O)O)N)[C@@H]([C@H]([C@@H]1O)O)NC(=O)C
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
- molecule: Monomer
element: H
position: 16
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
AA0100:
id: AA0100
name: L-valine amide
comments: 'Generating Enzyme: peptidylglycine monooxygenase (EC 1.14.17.3).'
synonyms:
- (2S)-2-amino-3-methylbutanamide
- (2S)-2-amino-3-methyl-butanamide
- valinamide
- valinylamine
- L-valinamide
- X
identifiers:
- ns: mod
id: MOD:00109
- ns: pdb-ccd
id: VLM
- ns: chebi
id: CHEBI:21418
- ns: cas
id: 4540-60-7
- ns: go
id: GO:0018053
- ns: resid
id: AA0100
- ns: pdb.ligand
id: NH2
structure: '[NH3+][C@H](C(=O)N)C(C)C'
base_monomers:
- V
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AA0474:
id: AA0474
name: L-serine 5-methyloxazole-4-carboxylic acid
comments: 'Formed by the condensation of a threonine hydroxyl with the carbonyl
of the preceding residue and alpha-beta dehydrogenation. Generating Enzyme:
peptidyl-threonine cyclase (EC 4.2.1.-); peptidyl-oxazoline dehydrogenase (EC
1.3.-.-).'
synonyms:
- 2-[1-azanyl-2-hydroxyethyl]-5-methyl-1,3-oxazole-4-carboxylic acid
- 2-[(1S)-1-amino-2-hydroxyethyl]-5-methyl-1,3-oxazole-4-carboxylic acid
identifiers:
- ns: mod
id: MOD:01397
- ns: resid
id: AA0474
structure: OC[C@@H](c1oc(c(n1)C(=O)O)C)N
base_monomers:
- S
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
AA0369:
id: AA0369
name: 3,4-dihydroxy-L-arginine
comments: Hydroxylations at C-3 and C-4 are assumed. Neither the positions of
the hydroxylations nor the stereochemistry for the chiral centers they produce
have been determined. The (2S,3R,4R) stereoisomer is shown.
synonyms:
- beta,gamma-dihydroxyarginine
- 2-amino-5-guanidino-3,4-dihydroxypentanoic acid
- (2S,3Xi,4Xi)-2-amino-5-carbamimidamido-3,4-dihydroxypentanoic acid
identifiers:
- ns: resid
id: AA0369
- ns: mod
id: MOD:00374
- ns: go
id: GO:0030961
structure: O[C@@H]([C@@H]([C@@H](C(=O)O)N)O)C[NH+]=C(N)N
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
AA0562:
id: AA0562
name: L-cysteinyl L-phenylalanine sulfenamide
comments: 'This cross-link is formed by the condensation of a cysteine residue
sulfhydryl with the alpha-amido of the following residue. Generating Enzyme:
autocatalytic.'
synonyms:
- 4-amino-3-isothiazolidinone-L-phenylalanine
- phenylalanine-cysteine sulfenyl amide cross-link
- 2-(4-amino-3-oxo-isothiazolidin-2-yl)-3-phenylpropanoic acid
- phenylalanine-cysteine sulphenyl amide cross-link
- cysteinyl phenylalanine sulfenamide
- (2S)-2-[(4R)-4-amino-3-oxo-1,2-thiazolidin-2-yl]-3-phenylpropanoic acid
identifiers:
- ns: resid
id: AA0562
- ns: mod
id: MOD:01859
structure: '[NH3+][C@H]1CSN(C1=O)[C@H](C(=O)O)Cc1ccccc1'
base_monomers:
- F
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
- molecule: Monomer
element: H
position: 16
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AA0267:
id: AA0267
name: O-(phospho-5'-adenosine)-L-threonine
synonyms:
- L-threonine monoanhydride with 5'-adenylic acid
- 5'-adenylic-O3-L-threonine
- O3-(phospho-5'-adenosine)-L-threonine
- O(gamma)-5'-adenylic-L-threonine
- beta-5'-adenylic-L-threonine
- O3-L-threonine 5'-adenosine phosphodiester
- (2S,3R)-2-amino-3-(5'-adenosine phosphonoxy)butanoic acid
identifiers:
- ns: resid
id: AA0267
- ns: mod
id: MOD:00272
- ns: go
id: GO:0018178
structure: OC(=O)[C@H]([C@H](OP(=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)[O-])C)[NH3+]
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 36
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 36
- molecule: Monomer
element: H
position: 36
charge: 1
AA0340:
id: AA0340
name: 2-(S-L-cysteinyl)-L-phenylalanine
comments: The L-stereoisomer of the 2-S-cysteinyl substituted phenylalanine has
R configuration.
synonyms:
- alpha-(L-cystein-S-yl)-L-phenylalanine
- (2R)-2-amino-2-[(2R)-2-amino-2-carboxyethyl]sulfanyl-3-phenylpropanoic acid
- (2R,5R)-2,5-diamino-3-thia-2-phenylmethylhexanedioic acid
identifiers:
- ns: go
id: GO:0046924
- ns: resid
id: AA0340
- ns: mod
id: MOD:00345
structure: O=C[C@@](Cc1ccccc1)(SC[C@@H](C(=O)O)[NH3+])N
base_monomers:
- F
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
- molecule: Monomer
element: H
position: 17
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
AA0569:
id: AA0569
name: N,N-dimethyl-L-arginine
comments: This modification should not be confused with omega-N,omega-N'-dimethyl-L-arginine
(see RESID:AA0067) or omega-N,omega-N-dimethyl-L-arginine (see RESID:AA0068).
synonyms:
- N(alpha),N(alpha)-dimethylarginine
- (2S)-5-carbamimidamido-2-(dimethylamino)pentanoic acid [tautomer]
- (2S)-5-[(diaminomethylidene)amino]-2-(dimethylamino)pentanoic acid
- N2,N2-dimethylarginine
identifiers:
- ns: mod
id: MOD:01898
- ns: cas
id: 190784-00-0
- ns: resid
id: AA0569
structure: C[NH+]([C@H](C(=O)O)CCC[NH+]=C(N)N)C
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
- molecule: Monomer
element: H
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
AA0107:
id: AA0107
name: S-diacylglycerol-L-cysteine
comments: The oleate and palmitate actually represent mixtures of saturated (generally
at 3') and unsaturated (generally at 2') fatty acids. The signal peptide that
is cleaved immediately before the modified cysteine typically ends in the motif
[ILMV]X[AGS]C. Cleavage and formation of this modification may occur without
N-palmitoylation, see RESID:AA0060.
synonyms:
- S-(1-2'-oleoyl-3'-palmitoyl-glycerol)cysteine
- (2R)-2-amino-3-[(2S)-2-((9Z)-9-octadecenoyloxy)-3-(hexadecanoyloxy)propyl]sulfanylpropanoic
acid
- 2-amino-3-[(S)-2-((Z)-9-octadecenoyloxy)-3-(hexadecanoyloxy)propyl]thiopropanoic
acid
identifiers:
- ns: go
id: GO:0018231
- ns: pdb.ligand
id: DGA
- ns: mod
id: MOD:00116
- ns: resid
id: AA0107
structure: CCCCCCCCCCCCCCCC(=O)OC[C@H](OC(=O)CCCCCCC/C=C\CCCCCCCC)CSC[C@@H](C(=O)O)[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 47
l_bond_atoms:
- molecule: Monomer
element: N
position: 50
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 49
- molecule: Monomer
element: H
position: 49
l_displaced_atoms:
- molecule: Monomer
element: H
position: 50
- molecule: Monomer
element: H
position: 50
charge: 1
AA0073:
id: AA0073
name: 3'-methyl-L-histidine
comments: 'In the older biochemical literature this is usually called 1-methylhistidine.
See also RESID:AA0317. The crystallographic designation for the substituted
nitrogen is delta-1, D1. Generating Enzyme: protein-histidine N(pi)-methyltransferase
(EC 2.1.1.-).'
synonyms:
- 1-methylhistidine [misnomer]
- H
- n1-methylated histidine
- N(delta)-methylhistidine
- (2S)-2-amino-3-(3-methyl-3H-imidazol-4-yl)propanoic acid
- pros-methylhistidine
- N(pi)-methylhistidine
- (2S)-2-amino-3-(3-methylimidazol-4-yl)propanoic acid
- 3-methyl-L-histidine
identifiers:
- ns: cas
id: 368-16-1
- ns: pdb-ccd
id: MHS
- ns: mod
id: MOD:00082
- ns: go
id: GO:0018021
- ns: resid
id: AA0073
- ns: chebi
id: CHEBI:43903
- ns: pdb.ligand
id: MHS
structure: Cn1cncc1C[C@H]([NH3+])C(=O)O
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
- molecule: Monomer
element: H
position: 16
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
AA0029:
id: AA0029
name: 3-hydroxy-L-proline
comments: 'There are at least three different genes for procollagen-proline 3-dioxygenase
in mammals with different specificities and patterns of tissue expression. Usually
proline 3-hydroxylation occurs at the second position of specific GPP sequences
in collagen chains and is preceded by proline 4-hydroxylation of the proline
in the third position. See RESID:AA0030. Generating Enzyme: procollagen-proline
3-dioxygenase (EC 1.14.11.7).'
synonyms:
- 3-trans-hydroxy-L-proline
- (3S)-3-hydroxy-L-proline
- L-threo-3-hydroxyproline
- beta-hydroxypyrrolidine-alpha-carboxylic acid
- P
- 3-hydroxyproline
- (2S,3S)-3-hydroxypyrrolidine-2-carboxylic acid
identifiers:
- ns: cas
id: 4298-08-2
- ns: chebi
id: CHEBI:16889
- ns: resid
id: AA0029
- ns: go
id: GO:0018400
- ns: pdb-ccd
id: HY3
- ns: pdb.ligand
id: HY3
- ns: mod
id: MOD:00038
structure: O[C@H]1CC[NH2+][C@@H]1C(=O)O
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
AA0513:
id: AA0513
name: trithiocystine
synonyms:
- (2R,2'R)-3,3'-pentasulfane-1,5-diylbis(2-aminopropanoic acid)
- bis(2-amino-2-carboxyethyl)pentasulfide
- 3,3'-pentathiobisalanine
identifiers:
- ns: pdb.ligand
id: S3H
- ns: mod
id: MOD:01616
- ns: resid
id: AA0513
structure: O=C[C@H](CSSSSSC[C@@H](C(=O)O)[NH3+])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
- molecule: Monomer
element: H
position: 16
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
AA0070:
id: AA0070
name: N4-methyl-L-asparagine
synonyms:
- N(gamma)-methylasparagine
- N-methyl-L-asparagine
- N-methylasparagine
- N
- (2S)-2-amino-N4-methylbutanediamic acid
- (2S)-2-amino-4-methylamino-4-oxo-butanoic acid
- beta-methylasparagine [misnomer]
- n-methyl asparagine
- beta-aspartyl methylamide
identifiers:
- ns: pdb.ligand
id: MEN
- ns: resid
id: AA0070
- ns: cas
id: 7175-34-0
- ns: pdb-ccd
id: MEN
- ns: chebi
id: CHEBI:61960
- ns: mod
id: MOD:00079
- ns: go
id: GO:0019710
structure: CNC(=O)C[C@@H](C(=O)O)N
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
AA0043:
id: AA0043
name: N-acetyl-L-cysteine
comments: See also RESID:AA0044.
synonyms:
- 2-acetylamino-3-sulfanylpropanoic acid
- 2-acetylamino-3-mercaptopropanoic acid
- N-acetylcysteine
- 2-acetylazanyl-3-sulfanylpropanoic acid
- (2R)-2-acetamido-3-sulfanylpropanoic acid
identifiers:
- ns: resid
id: AA0043
- ns: chebi
id: CHEBI:28939
- ns: go
id: GO:0018275
- ns: mod
id: MOD:00052
- ns: cas
id: 616-91-1
structure: SC[C@@H](C(=O)O)NC(=O)C
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
- molecule: Monomer
element: H
position: 7
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
AA0183:
id: AA0183
name: (Z)-2,3-didehydrotyrosine
synonyms:
- cis-dehydrotyrosine
- green fluorescent protein chromophore
- '{(4z)-2-[(1s)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1h-imidazol-1-yl}acetic
acid'
- MYG
- 2-[(4Z)-2-[(1S)-1-amino-3-methylsulfanyl-propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-imidazol-1-yl]ethanoic
acid
- para-hydroxybenzylidene-imidazolidinone chromophore
- '{(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid'
- red fluorescent protein chromophore
- (2Z)-2-amino-3-(4-hydroxyphenyl)prop-2-enoic acid
- amino-(para-hydroxybenzylidenyl)acetic acid
identifiers:
- ns: mod
id: MOD:00191
- ns: pdb-ccd
id: CH6
- ns: resid
id: AA0183
- ns: pdb.ligand
id: CH6
- ns: go
id: GO:0018251
structure: Oc1ccc(cc1)/C=C(/C(=O)O)\N
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
- molecule: Monomer
element: H
position: 12
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
AA0339:
id: AA0339
name: N-palmitoyl-glycine
comments: 'This modification should not be confused with N-myristoyl-glycine (see
RESID:AA0059). Generating Enzyme: glycylpeptide N-palmitoyltransferase (EC 2.3.1.-).'
synonyms:
- (hexadecanamido)acetic acid
- N-(1-oxohexadecyl)glycine
- (hexadecanoylamino)acetic acid
- (hexadecanoylamino)ethanoic acid
identifiers:
- ns: pdb.ligand
id: '140'
- ns: cas
id: 2441-41-0
- ns: go
id: GO:0046918
- ns: mod
id: MOD:00344
- ns: resid
id: AA0339
structure: CCCCCCCCCCCCCCCC(=O)NCC(=O)O
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
AA0547:
id: AA0547
name: (E)-dehydrobutyrine
comments: 'In some cases it has not been firmly established whether the natural
form is the Z or the E isomer. For the Z isomer, see RESID:AA0182. A 2,3-didehydro
amino acid blocks Edman degradation. Generating Enzyme: protein-threonine dehydratase
(EC 4.2.1.-).'
synonyms:
- 2,3-didehydrobutyrine
- (E)-2-amino-2-butenoic acid
- 3-methyldehydroalanine
- anhydrothreonine
- (2E)-2-aminobut-2-enoic acid
- Dhb
- (E)-2-aminobutenoic acid
- methyl-dehydroalanine
- alpha,beta-dehydroaminobutyric acid
identifiers:
- ns: resid
id: AA0547
- ns: mod
id: MOD:00190
structure: C/C=C(\C(=O)O)/N
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
AA0587:
id: AA0587
name: Desmosine
comments: 'After the oxidation of three of the four lysines to allysine (see RESID:AA0121),
this cross-link forms spontaneously with a Schiff-base reaction, and a series
of one aldimine and two aldol condensation reactions. In this aleatoric modification
up to four peptide chains may be crosslinked, with each peptide contributing
a lysine potentially in any of the four biosynthetic positions. Isodesmosine
is a structural isomer (see RESID:AA0588). Up to two of the lysines forming
the cross-link may also be hydroxylated and glycosylated (see RESID:AA0028 and
RESID:AA0153). Generating Enzyme: lysyl oxidase (EC 1.4.3.13).'
synonyms:
- 6-[4-(4-amino-4-carboxybutyl)-3,5-bis(3-amino-3-carboxypropyl)pyridinio]norleucine
- 4-[(4S)-4-amino-4-carboxybutyl]-1-[(5S)-5-amino-5-carboxypentyl]-3,5-bis[(3S)-3-amino-3-carboxypropyl]pyridinium
identifiers:
- ns: chebi
id: CHEBI:37629
- ns: mod
id: MOD:01933
- ns: cas
id: 11003-57-9
- ns: resid
id: AA0587
structure: O=C[C@H](CCC1=C[NH+](CCCC[C@@H](C(=O)O)[NH3+])C=C([C@H]1CCC[C@@H](C=O)[NH3+])CC[C@@H](C=O)[NH3+])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
- molecule: Monomer
element: H
position: 19
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
AA0419:
id: AA0419
name: N-methyl-L-proline
comments: 'Generating Enzyme: N-terminal RCC1 methyltransferase (EC 2.1.1.-).'
synonyms:
- 1-methylpyrrolidine-2-carboxylic acid
- (S)-1-methylpyrrolidine-2-carboxylic acid
- hygric acid
identifiers:
- ns: resid
id: AA0419
- ns: cas
id: 475-11-6
- ns: mod
id: MOD:00830
- ns: go
id: GO:0035568
structure: C[NH+]1CCC[C@H]1C(=O)O
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
- molecule: Monomer
element: H
position: 11
AA0473:
id: AA0473
name: 5-hydroxy-3-methyl-L-proline
comments: The stereochemistry at C3 and C5 has not been resolved, but (3S) can
be assumed by derivation from L-isoleucine. The (3S,5S) form is shown.
synonyms:
- beta-methyl-delta-hydroxyproline
- (2S,3S,5Xi)-5-hydroxy-3-methylpyrrolidine-2-carboxylic acid
- 5-hydroxy-3-methylproline
identifiers:
- ns: resid
id: AA0473
- ns: mod
id: MOD:01897
structure: C[C@H]1C[C@@H]([NH2+][C@@H]1C(=O)O)O
base_monomers:
- I
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
- molecule: Monomer
element: H
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
AA0143:
id: AA0143
name: S-(8alpha-FAD)-L-cysteine
comments: 'The arrangement of the attachment has not been completely established
in some cases. The keyword "phosphoprotein" is not used with flavin modifications
linked through the flavin. Generating Enzyme: autocatalytic.'
synonyms:
- (2R)-2-amino-3-[8alpha-riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester
with adenosine]sulfanylpropanoic acid
- 8alpha-(S-cysteinyl)FAD
identifiers:
- ns: resid
id: AA0143
- ns: pdb.ligand
id: FAD
- ns: go
id: GO:0018294
- ns: mod
id: MOD:00152
structure: O=C1[N-]C(=O)C2C(N1)N(C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O[P@](=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc3c1ncnc3N)[O-])[O-])O)O)O)C1C(N2)CC(C(C1)CSC[C@@H](C(=O)O)[NH3+])C
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 64
l_bond_atoms:
- molecule: Monomer
element: N
position: 67
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 66
- molecule: Monomer
element: H
position: 66
l_displaced_atoms:
- molecule: Monomer
element: H
position: 67
- molecule: Monomer
element: H
position: 67
charge: 1
AA0564:
id: AA0564
name: N6-(4-aminobutyl)-L-lysine
comments: 'Deoxyhypusine is generated as an intermediate modification of initiation
factor 5A, eIF5A, and as a modified lysine reaction intermediate in deoxyhypusine
synthase before transfer of the 4-aminobutyl group. Generating Enzyme: autocatalytic;
deoxyhypusine synthase (EC 2.5.1.46).'
synonyms:
- N6-(4-aminobutyl)lysine
- (2S)-2-amino-6-[(4-aminobutyl)amino]hexanoic acid
- deoxyhypusine
- (2S)-2-azanyl-6-(4-azanylbutylamino)hexanoic acid
- K
- N~6~-(4-aminobutyl)-L-lysine
identifiers:
- ns: pdb-ccd
id: 5GG
- ns: go
id: GO:0034038
- ns: cas
id: 82543-85-9
- ns: chebi
id: CHEBI:50038
- ns: resid
id: AA0564
- ns: mod
id: MOD:01880
structure: '[NH3+]CCCC[NH2+]CCCC[C@@H](C(=O)O)[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
- molecule: Monomer
element: H
position: 20
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
AA0101:
id: AA0101
name: L-cysteine methyl disulfide
synonyms:
- s-methyl-thio-cysteine
- (2R)-2-amino-3-(methyldisulfanediyl)propanoic acid
- 2-azanyl-3-(methyldisulfanediyl)-propanoic acid
- L-3-(methyldithio)alanine
- 2-amino-3-(methyldisulfanediyl)propanoic acid
- S-methylthio-L-cysteine
- S-methylthiocysteine
- C
- (2R)-2-azanyl-3-methyldisulfanyl-propanoic acid
- 2-amino-3-(methyldithio)propanoic acid
- 3-(methyldisulfanyl)-L-alanine
- 2-amino-3-methyldisulfanylpropanoic acid
identifiers:
- ns: go
id: GO:0018222
- ns: pdb-ccd
id: SCH
- ns: mod
id: MOD:00110
- ns: resid
id: AA0101
- ns: pdb.ligand
id: SCH
- ns: cas
id: 33784-54-2
structure: CSSC[C@H]([NH3+])C(=O)O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
- molecule: Monomer
element: H
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
AA0353:
id: AA0353
name: 3'-(8alpha-FMN)-L-histidine
comments: In a later publication the authors changed the enzyme activity, the
connection from a histidine nitrogen to a cysteine sulfur, and the identity
of the flavin from FMN to FAD. They now believe the modification is S-(8alpha-FAD)-L-cysteine,
see RESID:AA0143. The keyword "phosphoprotein" is not used with flavin modifications
linked through the flavin.
synonyms:
- (S)-2-amino-3-(3-[8alpha riboflavin 5'-dihydrogen phosphate]imidazol-4-yl)propanoic
acid
- pros-(8alpha-FMN)-histidine
- 8alpha-(N3'-histidyl)FMN
- N(pi)-(8alpha-FMN)-histidine
- 8alpha-(N(delta)-histidyl)FMN
identifiers:
- ns: mod
id: MOD:00358
- ns: go
id: GO:0050744
- ns: resid
id: AA0353
structure: O=C1[N-]C(=O)C2C(N1)N(C[C@@H]([C@@H]([C@@H](COP(=O)([O-])[O-])O)O)O)C1C(N2)CC(C(C1)Cn1cncc1C[C@@H](C(=O)O)[NH3+])C
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 42
l_bond_atoms:
- molecule: Monomer
element: N
position: 45
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 44
- molecule: Monomer
element: H
position: 44
l_displaced_atoms:
- molecule: Monomer
element: H
position: 45
- molecule: Monomer
element: H
position: 45
charge: 1
AA0291:
id: AA0291
name: O-D-glucuronosyl-L-serine
comments: 'The beta glucuronosyl form is shown. See also RESID:AA0154, RESID:AA0208,
RESID:AA0209, RESID:AA0210, RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398,
RESID:AA0400, RESID:AA0402, RESID:AA0404, RESID:AA0406, and RESID:AA0422 for
other O-glycosylated serines. Generating Enzyme: UDP-glucuronate beta-D-glucuronosyltransferase
(acceptor-unspecific) (EC 2.4.1.17).'
synonyms:
- O3-D-glucuronosyl-L-serine
- (2S)-2-amino-3-(beta-D-glucopyranuronosyl)propanoic acid
identifiers:
- ns: resid
id: AA0291
- ns: cas
id: 528-16-5
- ns: go
id: GO:0018413
- ns: mod
id: MOD:00296
structure: O=C[C@H](CO[C@H]1O[C@H](C(=O)[O-])[C@H]([C@@H]([C@H]1O)O)O)[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 24
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 24
- molecule: Monomer
element: H
position: 24
charge: 1
'004':
id: '004'
name: (2s)-amino(phenyl)ethanoic acid
synonyms:
- (2S)-amino(phenyl)ethanoic acid
- (2S)-2-azanyl-2-phenyl-ethanoic acid
identifiers:
- ns: pdb-ccd
id: '004'
structure: '[NH3+][C@@H](c1ccccc1)C(=O)[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
00B:
id: 00B
name: (4r)-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
synonyms:
- (4R)-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
identifiers:
- ns: pdb-ccd
id: 00B
structure: '[O-]C(=O)[C@H]1[NH2+]CSC1(C)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
01W:
id: 01W
name: (2s)-2-ammonio-4-[(2,4-dinitrophenyl)amino]butanoate
synonyms:
- (2S)-2-ammonio-4-[(2,4-dinitrophenyl)amino]butanoate
- (2S)-2-azaniumyl-4-[(2,4-dinitrophenyl)amino]butanoate
- X
identifiers:
- ns: pdb-ccd
id: 01W
structure: '[O-]C(=O)[C@H](CCNc1ccc(cc1[N+](=O)[O-])[N+](=O)[O-])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
02A:
id: 02A
name: (2s)-azetidine-2-carboxylic acid
synonyms:
- (2S)-azetidine-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: 02A
structure: '[O-]C(=O)[C@@H]1CC[NH2+]1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
02L:
id: 02L
name: n-(2,2-dimethylpropyl)-l-asparagine
synonyms:
- N
- N-(2,2-dimethylpropyl)-L-asparagine
- (2S)-2-azanyl-4-(2,2-dimethylpropylamino)-4-oxidanylidene-butanoic acid
identifiers:
- ns: pdb-ccd
id: 02L
structure: '[NH3+][C@H](C(=O)[O-])CC(=O)NCC(C)(C)C'
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
02O:
id: 02O
name: 3-(3-tert-butyl-1,2,4-oxadiazol-5-yl)-l-alanine
synonyms:
- 3-(3-tert-butyl-1,2,4-oxadiazol-5-yl)-L-alanine
- (2S)-2-azanyl-3-(3-tert-butyl-1,2,4-oxadiazol-5-yl)propanoic acid
identifiers:
- ns: pdb-ccd
id: 02O
structure: '[NH3+][C@H](C(=O)[O-])Cc1onc(n1)C(C)(C)C'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
02V:
id: 02V
name: (2s)-(3,4-dihydroxyphenyl)(methylamino)ethanoic acid
synonyms:
- (2S)-2-[3,4-bis(oxidanyl)phenyl]-2-(methylamino)ethanoic acid
- (2S)-(3,4-dihydroxyphenyl)(methylamino)ethanoic acid
identifiers:
- ns: pdb-ccd
id: 02V
structure: C[NH2+][C@@H](c1ccc(c(c1)O)O)C(=O)[O-]
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
02Y:
id: 02Y
name: 6-diazonio-5-oxo-l-norleucine
synonyms:
- 6-diazonio-5-oxo-L-norleucine
- (5S)-5-azanyl-6-oxidanyl-2,6-bis(oxidanylidene)hexane-1-diazonium
identifiers:
- ns: pdb-ccd
id: 02Y
structure: '[O-]C(=O)[C@@H]([NH3+])CCC(=O)C[N+]#N'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
'037':
id: '037'
name: (1s,3ar,6as)-octahydrocyclopenta[c]pyrrole-1-carboxylic acid
synonyms:
- (1S,3aR,6aS)-octahydrocyclopenta[c]pyrrole-1-carboxylic acid
- (3S,3aS,6aR)-1,2,3,3a,4,5,6,6a-octahydrocyclopenta[c]pyrrole-3-carboxylic acid
identifiers:
- ns: pdb-ccd
id: '037'
structure: '[O-]C(=O)[C@H]1[NH2+]C[C@H]2[C@@H]1CCC2'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
03Y:
id: 03Y
name: 2-methyl-l-cysteine
synonyms:
- 2-methyl-L-cysteine
- C
- (2R)-2-azanyl-2-methyl-3-sulfanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: 03Y
structure: '[O-]C(=O)[C@@]([NH3+])(CS)C'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
04U:
id: 04U
name: azanylidene-[(3s,5s)-5-carboxypyrrolidin-3-yl]imino-azanium
synonyms:
- (4S)-4-triaza-1,2-dien-2-ium-1-yl-L-proline
- P
- azanylidene-[(3S,5S)-5-carboxypyrrolidin-3-yl]imino-azanium
identifiers:
- ns: pdb-ccd
id: 04U
structure: '[N-]=[N+]=N[C@@H]1C[NH2+][C@@H](C1)C(=O)[O-]'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
04V:
id: 04V
name: (2s)-pyrrolidine-2-carboximidic acid
synonyms:
- P
- (2S)-pyrrolidine-2-carboximidic acid
identifiers:
- ns: pdb-ccd
id: 04V
structure: '[O-]C(=[NH2+])[C@@H]1CCC[NH2+]1'
base_monomers:
- P
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
04X:
id: 04X
name: (2s)-5-(morpholin-4-ylmethyl)-1,2,3,6-tetrahydropyridine-2-carboxylic acid
synonyms:
- (2S)-5-(morpholin-4-ylmethyl)-1,2,3,6-tetrahydropyridine-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: 04X
structure: '[O-]C(=O)[C@H]1[NH2+]CC(=CC1)CN1CCOCC1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
05N:
id: 05N
name: (3r,4r)-4-hydroxy-3-methyl-l-proline
synonyms:
- P
- (2S,3R,4R)-3-methyl-4-oxidanyl-pyrrolidine-2-carboxylic acid
- (3R,4R)-4-hydroxy-3-methyl-L-proline
identifiers:
- ns: pdb-ccd
id: 05N
structure: O[C@H]1C[NH2+][C@@H]([C@H]1C)C(=O)[O-]
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
07O:
id: 07O
name: s-[(2s)-2-phenylpropanoyl]-l-cysteine
synonyms:
- S-[(2S)-2-phenylpropanoyl]-L-cysteine
- (2R)-2-azanyl-3-[(2S)-2-phenylpropanoyl]sulfanyl-propanoic acid
- C
identifiers:
- ns: pdb-ccd
id: 07O
structure: C[C@@H](c1ccccc1)C(=O)SC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
08M:
id: 08M
name: n~5~-(pyrazin-2-ylcarbonyl)-l-ornithine
synonyms:
- (2S)-2-azanyl-5-(pyrazin-2-ylcarbonylamino)pentanoic acid
- N~5~-(pyrazin-2-ylcarbonyl)-L-ornithine
identifiers:
- ns: pdb-ccd
id: 08M
structure: '[O-]C(=O)[C@@H]([NH3+])CCCNC(=O)c1cnccn1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
0A0:
id: 0A0
name: 2-methyl-l-aspartic acid
synonyms:
- 2-methyl-L-aspartic acid
- D
- (2S)-2-amino-2-methyl-butanedioic acid
identifiers:
- ns: pdb-ccd
id: 0A0
structure: '[O-]C(=O)C[C@@](C(=O)[O-])([NH3+])C'
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
0A1:
id: 0A1
name: o-methyl-l-tyrosine
synonyms:
- O-methyl-L-tyrosine
- (2S)-2-amino-3-(4-methoxyphenyl)propanoic acid
- Y
identifiers:
- ns: pdb-ccd
id: 0A1
structure: COc1ccc(cc1)C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
0A2:
id: 0A2
name: '[(1r)-1,5-diaminopentyl][bis(ethanolato)]hydroxyborate(1-)'
synonyms:
- K
- '[(1R)-1,5-diaminopentyl]-diethoxy-hydroxy-boron'
- '[(1R)-1,5-diaminopentyl][bis(ethanolato)]hydroxyborate(1-)'
identifiers:
- ns: pdb-ccd
id: 0A2
structure: CCO[B-]([C@H](CCCC[NH3+])[NH3+])(OCC)O
base_monomers:
- K
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
0A8:
id: 0A8
name: s-[(2-chloroethyl)carbamoyl]-l-cysteine
synonyms:
- (2R)-2-amino-3-(2-chloroethylcarbamoylsulfanyl)propanoic acid
- S-[(2-chloroethyl)carbamoyl]-L-cysteine
- C
identifiers:
- ns: pdb-ccd
id: 0A8
structure: '[O-]C(=O)[C@@H]([NH3+])CSC(=O)NCCCl'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
0A9:
id: 0A9
name: methyl l-phenylalaninate
synonyms:
- methyl L-phenylalaninate
- methyl (2S)-2-azanyl-3-phenyl-propanoate
identifiers:
- ns: pdb-ccd
id: 0A9
structure: COC(=O)[C@H](Cc1ccccc1)N
base_monomers:
- F
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
0AB:
id: 0AB
name: (3s,4s)-3-amino-4-methyl-3,4-dihydro-2h-pyran-2-one
synonyms:
- V
- (3S,4S)-3-amino-4-methyl-3,4-dihydropyran-2-one
- (3S,4S)-3-amino-4-methyl-3,4-dihydro-2H-pyran-2-one
identifiers:
- ns: pdb-ccd
id: 0AB
structure: O=C1OC=C[C@@H]([C@@H]1[NH3+])C
base_monomers:
- V
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
0AH:
id: 0AH
name: o-(bromoacetyl)-l-serine
synonyms:
- O-(bromoacetyl)-L-serine
- S
- (2S)-2-amino-3-(2-bromoethanoyloxy)propanoic acid
identifiers:
- ns: pdb-ccd
id: 0AH
structure: '[O-]C(=O)[C@@H]([NH3+])COC(=O)CBr'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
0AK:
id: 0AK
name: (2s)-2-amino-4-(2-chloroethoxy)-4-oxobutanoic acid
synonyms:
- D
- (2S)-2-amino-4-(2-chloroethoxy)-4-oxo-butanoic acid
- (2S)-2-amino-4-(2-chloroethoxy)-4-oxobutanoic acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: 0AK
structure: '[O-]C(=O)[C@@H]([NH3+])CC(=O)OCCCl'
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
0AR:
id: 0AR
name: n-[n-[(4s)-4-azanyl-5-hydroxy-5-oxo-pentyl]carbamimidoyl]ethanamide
synonyms:
- N~5~-(N-acetylcarbamimidoyl)-L-ornithine
- (2S)-2-azanyl-5-[(N-ethanoylcarbamimidoyl)amino]pentanoic acid
- R
identifiers:
- ns: pdb-ccd
id: 0AR
structure: CC(=O)NC(=[NH2+])NCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
0BN:
id: 0BN
name: 4-carbamimidoyl-l-phenylalanine
synonyms:
- F
- (2S)-2-azanyl-3-(4-carbamimidoylphenyl)propanoic acid
- 4-carbamimidoyl-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: 0BN
structure: '[O-]C(=O)[C@H](Cc1ccc(cc1)C(=[NH2+])N)[NH3+]'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
0CS:
id: 0CS
name: 3-[(s)-hydroperoxysulfinyl]-l-alanine
synonyms:
- A
- (2R)-2-amino-3-[(S)-hydroperoxysulfinyl]propanoic acid
- 3-[(S)-hydroperoxysulfinyl]-L-alanine
identifiers:
- ns: pdb-ccd
id: 0CS
structure: '[O-]C(=O)[C@@H]([NH3+])C[S@@](=O)OO'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
'0E5':
id: '0E5'
name: (2s,3r)-2-azanyl-3-methyl-3-oxidanyl-pentanoic acid
synonyms:
- (2S,3R)-2-azanyl-3-methyl-3-oxidanyl-pentanoic acid
- T
- (2S,3S)-2-amino-3-hydroxy-3-methylpentanoic acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: '0E5'
structure: '[O-]C(=O)[C@@H]([NH3+])[C@@](CC)(O)C'
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
0EA:
id: 0EA
name: (betar)-beta,3-dihydroxy-n-methyl-l-tyrosine
synonyms:
- (betaR)-beta,3-dihydroxy-N-methyl-L-tyrosine
- (2S,3R)-3-[3,4-bis(oxidanyl)phenyl]-2-(methylamino)-3-oxidanyl-propanoic acid
- Y
identifiers:
- ns: pdb-ccd
id: 0EA
structure: C[NH2+][C@@H]([C@@H](c1ccc(c(c1)O)O)O)C(=O)[O-]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
0FL:
id: 0FL
name: 3-amino-n-formyl-l-alanine
synonyms:
- A
- 3-amino-N-formyl-L-alanine
- (2S)-3-azanyl-2-formamido-propanoic acid
identifiers:
- ns: pdb-ccd
id: 0FL
structure: O=CN[C@H](C(=O)[O-])C[NH3+]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 3
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 3
0G5:
id: 0G5
name: n~5~-(3-iodobenzoyl)-l-ornithine
synonyms:
- (2S)-2-azanyl-5-[(3-iodanylphenyl)carbonylamino]pentanoic acid
- N~5~-(3-iodobenzoyl)-L-ornithine
identifiers:
- ns: pdb-ccd
id: 0G5
structure: '[O-]C(=O)[C@H](CCCNC(=O)c1cccc(c1)I)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
0LF:
id: 0LF
name: (4r)-4-(4-phenylbutoxy)-l-proline
synonyms:
- (4R)-4-(4-phenylbutoxy)-L-proline
- (2S,4R)-4-(4-phenylbutoxy)pyrrolidine-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: 0LF
structure: '[O-]C(=O)[C@H]1[NH2+]C[C@@H](C1)OCCCCc1ccccc1'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
0NC:
id: 0NC
name: n-methyl-l-alaninamide
synonyms:
- A
- (2S)-2-amino-N-methyl-propanamide
- N-methyl-L-alaninamide
identifiers:
- ns: pdb-ccd
id: 0NC
structure: CNC(=O)[C@@H]([NH3+])C
base_monomers:
- A
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
0PR:
id: 0PR
name: n-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-l-tyrosine
synonyms:
- (2S)-2-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-(4-hydroxyphenyl)propanoic
acid
- Y
- N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-tyrosine
identifiers:
- ns: pdb-ccd
id: 0PR
structure: '[O-]C(=O)[C@H](Cc1ccc(cc1)O)[NH2+]Cc1c(cnc(c1O)C)COP(=O)([O-])[O-]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
0QL:
id: 0QL
name: 3-[(2-aminoethyl)disulfanyl]-l-alanine
synonyms:
- 3-[(2-aminoethyl)disulfanyl]-L-alanine
- (2R)-2-azanyl-3-(2-azanylethyldisulfanyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: 0QL
structure: '[O-]C(=O)[C@@H]([NH3+])CSSCC[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
0RJ:
id: 0RJ
name: 3-(formylamino)-l-alanine
synonyms:
- (2S)-2-azanyl-3-formamido-propanoic acid
- 3-(formylamino)-L-alanine
identifiers:
- ns: pdb-ccd
id: 0RJ
structure: O=CNC[C@@H](C(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
0TD:
id: 0TD
name: (3s)-3-(methylsulfanyl)-l-aspartic acid
synonyms:
- (3S)-3-(methylsulfanyl)-L-aspartic acid
- (2R,3S)-2-azanyl-3-methylsulfanyl-butanedioic acid
identifiers:
- ns: pdb-ccd
id: 0TD
structure: CS[C@@H]([C@@H](C(=O)[O-])[NH3+])C(=O)[O-]
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
0W6:
id: 0W6
name: (4s)-4-aminopentanoic acid
synonyms:
- (4S)-4-azanylpentanoic acid
- (4S)-4-aminopentanoic acid
identifiers:
- ns: pdb-ccd
id: 0W6
structure: '[O-]C(=O)CC[C@@H]([NH3+])C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
0WZ:
id: 0WZ
name: 3-(1h-pyrazol-1-yl)-l-tyrosine
synonyms:
- (2S)-2-azanyl-3-(4-oxidanyl-3-pyrazol-1-yl-phenyl)propanoic acid
- Y
- 3-(1H-pyrazol-1-yl)-L-tyrosine
identifiers:
- ns: pdb-ccd
id: 0WZ
structure: '[O-]C(=O)[C@H](Cc1ccc(c(c1)n1cccn1)O)[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
0X9:
id: 0X9
name: n~2~-sulfamoyl-l-arginine
synonyms:
- N~2~-sulfamoyl-L-arginine
- (2S)-5-carbamimidamido-2-(sulfamoylamino)pentanoic acid
identifiers:
- ns: pdb-ccd
id: 0X9
structure: '[O-]C(=O)[C@@H](NS(=O)(=O)N)CCCNC(=[NH2+])N'
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
0Y8:
id: 0Y8
name: (4r)-4-[(7-bromoisoquinolin-1-yl)oxy]-l-proline
synonyms:
- P
- (4R)-4-[(7-bromoisoquinolin-1-yl)oxy]-L-proline
- (2S,4R)-4-(7-bromanylisoquinolin-1-yl)oxypyrrolidine-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: 0Y8
structure: '[O-]C(=O)[C@H]1[NH2+]C[C@@H](C1)Oc1nccc2c1cc(Br)cc2'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
0YG:
id: 0YG
name: n-[(2z)-2-amino-3-(4-hydroxyphenyl)prop-2-enoyl]glycine
synonyms:
- YG
- 2-[[(Z)-2-azanyl-3-(4-hydroxyphenyl)prop-2-enoyl]amino]ethanoic acid
identifiers:
- ns: pdb-ccd
id: 0YG
structure: N/C(=C\c1ccc(cc1)O)/C(=O)NCC(=O)[O-]
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
11Q:
id: 11Q
name: 1-(cyclohexylmethyl)-l-proline
synonyms:
- 1-(cyclohexylmethyl)-L-proline
- (2S)-1-(cyclohexylmethyl)pyrrolidine-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: 11Q
structure: '[O-]C(=O)[C@@H]1CCC[NH+]1CC1CCCCC1'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
11W:
id: 11W
name: (4r)-4-[(2e)-3-{4-[(e)-phenyldiazenyl]phenyl}prop-2-en-1-yl]-l-glutamic
acid
synonyms:
- (2S,4R)-2-azanyl-4-[(E)-3-[4-[(E)-phenyldiazenyl]phenyl]prop-2-enyl]pentanedioic
acid
- (4R)-4-[(2E)-3-{4-[(E)-phenyldiazenyl]phenyl}prop-2-en-1-yl]-L-glutamic acid
identifiers:
- ns: pdb-ccd
id: 11W
structure: '[NH3+][C@H](C(=O)[O-])C[C@H](C(=O)[O-])C/C=C/c1ccc(cc1)/N=N/c1ccccc1'
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
12L:
id: 12L
name: (1r,2s,5s)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxylic acid
synonyms:
- (1R,2S,5S)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxylic acid
- (1S,4S,5R)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-4-carboxylic acid
identifiers:
- ns: pdb-ccd
id: 12L
structure: '[O-]C(=O)[C@H]1[NH2+]C[C@H]2[C@@H]1C2(C)C'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
12X:
id: 12X
name: (4r)-4-[(8-bromo-7-methoxy-2-{2-[(2-methylpropanoyl)amino]-1,3-thiazol-4-yl}quinolin-4-yl)oxy]-l-proline
synonyms:
- (4R)-4-[(8-bromo-7-methoxy-2-{2-[(2-methylpropanoyl)amino]-1,3-thiazol-4-yl}quinolin-4-yl)oxy]-L-proline
- (2S,4R)-4-[8-bromanyl-7-methoxy-2-[2-(2-methylpropanoylamino)-1,3-thiazol-4-yl]quinolin-4-yl]oxypyrrolidine-2-carboxylic
acid
identifiers:
- ns: pdb-ccd
id: 12X
structure: COc1ccc2c(c1Br)nc(cc2O[C@H]1C[NH2+][C@@H](C1)C(=O)[O-])c1csc(n1)NC(=O)C(C)C
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 24
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
12Y:
id: 12Y
name: (4r)-4-[(7-methoxy-2-{2-[(2-methylpropanoyl)amino]-1,3-thiazol-4-yl}quinolin-4-yl)oxy]-l-proline
synonyms:
- (2S,4R)-4-[7-methoxy-2-[2-(2-methylpropanoylamino)-1,3-thiazol-4-yl]quinolin-4-yl]oxypyrrolidine-2-carboxylic
acid
- (4R)-4-[(7-methoxy-2-{2-[(2-methylpropanoyl)amino]-1,3-thiazol-4-yl}quinolin-4-yl)oxy]-L-proline
identifiers:
- ns: pdb-ccd
id: 12Y
structure: COc1ccc2c(c1)nc(cc2O[C@H]1C[NH2+][C@@H](C1)C(=O)[O-])c1csc(n1)NC(=O)C(C)C
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 23
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
13E:
id: 13E
name: n-[(2s)-2-amino-3-phenylpropyl]-l-methionine
synonyms:
- N-[(2S)-2-amino-3-phenylpropyl]-L-methionine
- (2S)-2-[[(2S)-2-azanyl-3-phenyl-propyl]amino]-4-methylsulfanyl-butanoic acid
identifiers:
- ns: pdb-ccd
id: 13E
structure: CSCC[C@@H](C(=O)[O-])[NH2+]C[C@H](Cc1ccccc1)[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
'143':
id: '143'
name: s-2,3-dihydro-5-glycin-2-yl-isoxazol-3-yl-cysteine
synonyms:
- (2R)-2-amino-3-[[(3R)-5-[(1S)-1-amino-2-hydroxy-2-oxo-ethyl]-2,3-dihydro-1,2-oxazol-3-yl]sulfanyl]propanoic
acid
- S-{(3R)-5-[(S)-amino(carboxy)methyl]-2,3-dihydroisoxazol-3-yl}-L-cysteine
- C
identifiers:
- ns: pdb-ccd
id: '143'
structure: '[O-]C(=O)[C@H](CS[C@H]1NOC(=C1)[C@@H](C(=O)[O-])[NH3+])[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
'175':
id: '175'
name: 3,5-dihydro-5-methylidene-4h-imidazol-4-on
synonyms:
- 2-[2-[(1S)-1-aminoethyl]-4-(aminomethyl)-5-oxo-imidazolidin-1-yl]ethanoic acid
- '[(2S,4S)-2-[(1S)-1-aminoethyl]-4-(aminomethyl)-5-oxoimidazolidin-1-yl]acetic
acid'
- ASG
identifiers:
- ns: pdb-ccd
id: '175'
structure: '[O-]C(=O)CN1C(NC(C1=O)C[NH3+])[C@@H]([NH3+])C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
'193':
id: '193'
name: (2s)-4-(beta-alanylamino)-2-aminobutanoic acid
synonyms:
- (2S)-4-(beta-alanylamino)-2-aminobutanoic acid
- X
- (2S)-2-amino-4-(3-aminopropanoylamino)butanoic acid
identifiers:
- ns: pdb-ccd
id: '193'
structure: '[O-]C(=O)[C@@H]([NH3+])CCNC(=O)CC[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
19W:
id: 19W
name: 5-(aminooxy)-l-norvaline
synonyms:
- 5-(aminooxy)-L-norvaline
- (2S)-2-azanyl-5-azanyloxy-pentanoic acid
identifiers:
- ns: pdb-ccd
id: 19W
structure: NOCCC[C@@H](C(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
1C3:
id: 1C3
name: 1-(3,4,5-trimethoxybenzyl)-l-proline
synonyms:
- (2S)-1-[(3,4,5-trimethoxyphenyl)methyl]pyrrolidine-2-carboxylic acid
- 1-(3,4,5-trimethoxybenzyl)-L-proline
identifiers:
- ns: pdb-ccd
id: 1C3
structure: COc1cc(CN2CCC[C@H]2C(=O)[O-])cc(c1OC)OC
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
'1E3':
id: '1E3'
name: (2s)-2,9-diaminononanoic acid
synonyms:
- (2S)-2,9-diaminononanoic acid
- (2S)-2,9-bis(azanyl)nonanoic acid
identifiers:
- ns: pdb-ccd
id: '1E3'
structure: '[NH3+]CCCCCCC[C@@H](C(=O)[O-])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
1G2:
id: 1G2
name: (2s)-2-azido-3-phenylpropanoic acid
synonyms:
- (2S)-2-azido-3-phenyl-propanoic acid
- (2S)-2-azido-3-phenylpropanoic acid
identifiers:
- ns: pdb-ccd
id: 1G2
structure: '[O-]C(=O)[C@@H](N=[N+]=[N-])Cc1ccccc1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
1G3:
id: 1G3
name: (2s)-1-[4-(aminomethyl)phenyl]-4-(methylsulfonyl)butan-2-amine
synonyms:
- (2S)-1-[4-(aminomethyl)phenyl]-4-methylsulfonyl-butan-2-amine
- (2S)-1-[4-(aminomethyl)phenyl]-4-(methylsulfonyl)butan-2-amine
identifiers:
- ns: pdb-ccd
id: 1G3
structure: '[NH3+]Cc1ccc(cc1)C[C@@H](CCS(=O)(=O)C)[NH3+]'
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
1ME:
id: 1ME
name: (2s)-2-amino-3-methylsulfanyl-butanoic acid
synonyms:
- (2S)-2-amino-3-methylsulfanyl-butanoic acid
identifiers:
- ns: pdb-ccd
id: 1ME
structure: CSC([C@H](C(=O)[O-])[NH3+])C
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
1MH:
id: 1MH
name: 3-pyridin-3-yl-l-alanine
synonyms:
- (2S)-2-azanyl-3-pyridin-3-yl-propanoic acid
- 3-pyridin-3-yl-L-alanine
identifiers:
- ns: pdb-ccd
id: 1MH
structure: '[O-]C(=O)[C@H](Cc1cccnc1)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
1OP:
id: 1OP
name: o-(5-hydroxypentyl)-l-tyrosine
synonyms:
- O-(5-hydroxypentyl)-L-tyrosine
- Y
- (2S)-2-azanyl-3-[4-(5-oxidanylpentoxy)phenyl]propanoic acid
identifiers:
- ns: pdb-ccd
id: 1OP
structure: OCCCCCOc1ccc(cc1)C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
1PA:
id: 1PA
name: 4-(carboxymethyl)-l-phenylalanine
synonyms:
- F
- (2S)-2-azanyl-3-[4-(carboxymethyl)phenyl]propanoic acid
- 4-(carboxymethyl)-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: 1PA
structure: '[O-]C(=O)Cc1ccc(cc1)C[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
1PI:
id: 1PI
name: (3r)-3-[(2s)-2-amino-3-oxopropyl]piperidine-1-carboximidamide
synonyms:
- A
- (3R)-3-[(2S)-2-amino-3-oxopropyl]piperidine-1-carboximidamide
- (3R)-3-[(2S)-2-azanyl-3-oxo-propyl]piperidine-1-carboximidamide
identifiers:
- ns: pdb-ccd
id: 1PI
structure: '[O-]C(=O)[C@H](C[C@H]1CCCN(C1)C(=[NH2+])N)[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
1TQ:
id: 1TQ
name: 6-(formylamino)-7-hydroxy-l-tryptophan
synonyms:
- 6-(formylamino)-7-hydroxy-L-tryptophan
- (2S)-2-amino-3-(6-formamido-7-hydroxy-1H-indol-3-yl)propanoic acid
- W
identifiers:
- ns: pdb-ccd
id: 1TQ
structure: O=CNc1ccc2c(c1O)[nH]cc2C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
1TX:
id: 1TX
name: (2s)-2-amino-7-methoxy-7-oxoheptanoic acid
synonyms:
- (2S)-2-azanyl-7-methoxy-7-oxidanylidene-heptanoic acid
- (2S)-2-amino-7-methoxy-7-oxoheptanoic acid
identifiers:
- ns: pdb-ccd
id: 1TX
structure: COC(=O)CCCC[C@@H](C(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
1TY:
id: 1TY
name: 3-{(3e)-4-hydroxy-6-oxo-3-[(2-phenylethyl)imino]cyclohexa-1,4-dien-1-yl}alanine
synonyms:
- (2S)-2-amino-3-[(3E)-4-hydroxy-6-oxo-3-phenethylimino-1-cyclohexa-1,4-dienyl]propanoic
acid
- 3-{(3E)-4-hydroxy-6-oxo-3-[(2-phenylethyl)imino]cyclohexa-1,4-dien-1-yl}-L-alanine
- Y
identifiers:
- ns: pdb-ccd
id: 1TY
structure: '[NH3+][C@H](C(=O)[O-])CC1=C/C(=N\CCc2ccccc2)/C(=CC1=O)[O-]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
1U8:
id: 1U8
name: (3s)-3-amino-5-[(2,6-dimethylbenzoyl)oxy]-4-oxopentanoic acid
synonyms:
- (3S)-3-amino-5-[(2,6-dimethylbenzoyl)oxy]-4-oxopentanoic acid
- (3S)-3-azanyl-5-(2,6-dimethylphenyl)carbonyloxy-4-oxidanylidene-pentanoic acid
identifiers:
- ns: pdb-ccd
id: 1U8
structure: '[O-]C(=O)C[C@@H](C(=O)COC(=O)c1c(C)cccc1C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
1VR:
id: 1VR
name: (3r)-3-amino-4-methylpentanoic acid
synonyms:
- (3R)-3-amino-4-methylpentanoic acid
- (3R)-3-azanyl-4-methyl-pentanoic acid
identifiers:
- ns: pdb-ccd
id: 1VR
structure: '[NH3+][C@@H](C(C)C)CC(=O)[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
1X6:
id: 1X6
name: o-[(2e)-3-aminoprop-2-enoyl]-l-serine
synonyms:
- S
- O-[(2E)-3-aminoprop-2-enoyl]-L-serine
- (2S)-2-azanyl-3-[(E)-3-azanylprop-2-enoyl]oxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: 1X6
structure: '[O-]C(=O)[C@@H]([NH3+])COC(=O)/C=C/N'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
1XW:
id: 1XW
name: (1as,4s,6ar,7as)-octahydro-1h-cyclopropa[4,5]pyrrolo[1,2-a]pyrazine-4-carboxylic
acid
synonyms:
- (1aS,4S,6aR,7aS)-1a,3,4,5,6,6a,7,7a-octahydro-1H-cyclopropa[3,4]pyrrolo[3,5-b]pyrazine-4-carboxylic
acid
- (1aS,4S,6aR,7aS)-octahydro-1H-cyclopropa[4,5]pyrrolo[1,2-a]pyrazine-4-carboxylic
acid
identifiers:
- ns: pdb-ccd
id: 1XW
structure: '[O-]C(=O)[C@H]1NC[C@@H]2[NH+](C1)[C@H]1C[C@H]1C2'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
'200':
id: '200'
name: 4-chloro-l-phenylalanine
synonyms:
- F
- 4-chloro-L-phenylalanine
- (2S)-2-amino-3-(4-chlorophenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: '200'
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)Cl'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
22G:
id: 22G
name: n-[(2s)-2-amino-3-phenylpropyl]-l-tyrosine
synonyms:
- (2S)-2-[[(2S)-2-azanyl-3-phenyl-propyl]amino]-3-(4-hydroxyphenyl)propanoic acid
- N-[(2S)-2-amino-3-phenylpropyl]-L-tyrosine
identifiers:
- ns: pdb-ccd
id: 22G
structure: '[O-]C(=O)[C@H](Cc1ccc(cc1)O)[NH2+]C[C@H](Cc1ccccc1)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
23P:
id: 23P
name: 3-(propanoylamino)-l-alanine
synonyms:
- (2S)-2-azanyl-3-(propanoylamino)propanoic acid
- 3-(propanoylamino)-L-alanine
identifiers:
- ns: pdb-ccd
id: 23P
structure: '[O-]C(=O)[C@@H]([NH3+])CNC(=O)CC'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
23S:
id: 23S
name: (s)-2-amino-3-(6h-selenolo[2,3-b]-pyrrol-4-yl)-propionic acid
synonyms:
- (2S)-2-amino-3-(6H-selenopheno[3,2-d]pyrrol-4-yl)propanoic acid
- X
- 3-(6H-selenopheno[2,3-b]pyrrol-4-yl)-L-alanine
identifiers:
- ns: pdb-ccd
id: 23S
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1c[nH]c2c1cc[se]2'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
26B:
id: 26B
name: o-tert-butyl-n-[(3-{[(2,4,6-trimethylphenyl)carbamoyl]amino}naphthalen-2-yl)carbonyl]-l-threonine
synonyms:
- O-tert-butyl-N-[(3-{[(2,4,6-trimethylphenyl)carbamoyl]amino}naphthalen-2-yl)carbonyl]-L-threonine
- T
- (2S,3R)-3-[(2-methylpropan-2-yl)oxy]-2-[[3-[(2,4,6-trimethylphenyl)carbamoylamino]naphthalen-2-yl]carbonylamino]butanoic
acid
identifiers:
- ns: pdb-ccd
id: 26B
structure: O=C(Nc1c(C)cc(cc1C)C)Nc1cc2ccccc2cc1C(=O)N[C@@H]([C@H](OC(C)(C)C)C)C(=O)[O-]
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 37
l_bond_atoms:
- molecule: Monomer
element: N
position: 26
r_displaced_atoms:
- molecule: Monomer
element: O
position: 39
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 26
28X:
id: 28X
name: o-[(r)-{[(3r)-3,4-dihydroxybutyl]oxy}(hydroxy)phosphoryl]-l-threonine
synonyms:
- (2S,3R)-2-azanyl-3-[[(3R)-3,4-bis(oxidanyl)butoxy]-oxidanyl-phosphoryl]oxy-butanoic
acid
- O-[(R)-{[(3R)-3,4-dihydroxybutyl]oxy}(hydroxy)phosphoryl]-L-threonine
identifiers:
- ns: pdb-ccd
id: 28X
structure: OC[C@@H](CCOP(=O)(O[C@@H]([C@@H](C(=O)[O-])[NH3+])C)[O-])O
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
2AD:
id: 2AD
name: 2'-amino-2'-deoxyadenosine
synonyms:
- (2R,3S,4R,5R)-4-amino-5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-ol
- X
- 2'-amino-2'-deoxyadenosine
identifiers:
- ns: pdb-ccd
id: 2AD
structure: OC[C@H]1O[C@H]([C@@H]([C@@H]1O)[NH3+])n1cnc2c1ncnc2N
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
2AG:
id: 2AG
name: (2s)-2-aminopent-4-enoic acid
synonyms:
- A
- (2S)-2-azanylpent-4-enoic acid
- (2S)-2-aminopent-4-enoic acid
identifiers:
- ns: pdb-ccd
id: 2AG
structure: '[O-]C(=O)[C@@H]([NH3+])CC=C'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
2AS:
id: 2AS
name: (2s,3s)-3-methyl-aspartic acid
synonyms:
- (3S)-3-methyl-L-aspartic acid
- (2S,3S)-2-azanyl-1,4-dihydroxy-3-methyl-butane-1,1-dione
- X
identifiers:
- ns: pdb-ccd
id: 2AS
structure: O[C][C@H]([C@@H]([C](=O)(=O)O)N)C
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
2CO:
id: 2CO
name: s-hydroperoxycysteine
synonyms:
- S-hydroperoxy-L-cysteine
- (2R)-2-amino-3-hydroperoxysulfanyl-propanoic acid
- C
identifiers:
- ns: pdb-ccd
id: 2CO
structure: '[O-]C(=O)[C@@H]([NH3+])CSOO'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
2DO:
id: 2DO
name: (2s)-2-aminohexane-1,1-diol
synonyms:
- (2S)-2-aminohexane-1,1-diol
- X
identifiers:
- ns: pdb-ccd
id: 2DO
structure: CCCC[C@@H](C(O)O)[NH3+]
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
2FM:
id: 2FM
name: s-(difluoromethyl)homocysteine
synonyms:
- M
- (2S)-2-amino-4-(difluoromethylsulfanyl)butanoic acid
- difluoro-L-methionine
identifiers:
- ns: pdb-ccd
id: 2FM
structure: FC(SCC[C@@H](C(=O)[O-])[NH3+])F
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
2GX:
id: 2GX
name: beta-phenyl-l-phenylalanine
synonyms:
- (2S)-2-azanyl-3,3-diphenyl-propanoic acid
- beta-phenyl-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: 2GX
structure: '[NH3+][C@@H](C(c1ccccc1)c1ccccc1)C(=O)[O-]'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
2HF:
id: 2HF
name: 2-fluoro-l-histidine
synonyms:
- (2S)-2-azanyl-3-(2-fluoro-1H-imidazol-3-ium-4-yl)propanoic acid
- H
- 3-(2-fluoro-1H-imidazol-3-ium-4-yl)-L-alanine
identifiers:
- ns: pdb-ccd
id: 2HF
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1c[nH]c(n1)F'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
2JC:
id: 2JC
name: n-ethylglycine
synonyms:
- 2-(ethylamino)ethanoic acid
- N-ethylglycine
identifiers:
- ns: pdb-ccd
id: 2JC
structure: '[O-]C(=O)C[NH2+]CC'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
2JF:
id: 2JF
name: (2s)-2-amino-3-oxopropyl 4-{[(2s)-2-hydroxy-4-methylpentanoyl]amino}butanoate
synonyms:
- '[(2S)-2-azanyl-3-oxidanylidene-propyl] 4-[[(2S)-4-methyl-2-oxidanyl-pentanoyl]amino]butanoate'
- (2S)-2-amino-3-oxopropyl 4-{[(2S)-2-hydroxy-4-methylpentanoyl]amino}butanoate
identifiers:
- ns: pdb-ccd
id: 2JF
structure: CC(C[C@@H](C(=O)NCCCC(=O)OC[C@@H](C(=O)[O-])[NH3+])O)C
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
2JG:
id: 2JG
name: (2s)-2-amino-3-oxopropyl hexanoate
synonyms:
- '[(2S)-2-azanyl-3-oxidanylidene-propyl] hexanoate'
- (2S)-2-amino-3-oxopropyl hexanoate
identifiers:
- ns: pdb-ccd
id: 2JG
structure: CCCCCC(=O)OC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
2JH:
id: 2JH
name: 3-cyclobutyl-l-alanine
synonyms:
- (2S)-2-azanyl-3-cyclobutyl-propanoic acid
- 3-cyclobutyl-L-alanine
identifiers:
- ns: pdb-ccd
id: 2JH
structure: '[NH3+][C@H](C(=O)[O-])CC1CCC1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
2KK:
id: 2KK
name: n~6~-(4-fluorobenzoyl)-l-lysine
synonyms:
- N~6~-(4-fluorobenzoyl)-L-lysine
- K
- (2S)-2-azanyl-6-[(4-fluorophenyl)carbonylamino]hexanoic acid
identifiers:
- ns: pdb-ccd
id: 2KK
structure: '[NH3+][C@H](C(=O)[O-])CCCCNC(=O)c1ccc(cc1)F'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
2KP:
id: 2KP
name: n~6~-(4-bromobenzoyl)-l-lysine
synonyms:
- (2S)-2-azanyl-6-[(4-bromophenyl)carbonylamino]hexanoic acid
- K
- N~6~-(4-bromobenzoyl)-L-lysine
identifiers:
- ns: pdb-ccd
id: 2KP
structure: '[NH3+][C@H](C(=O)[O-])CCCCNC(=O)c1ccc(cc1)Br'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
2KY:
id: 2KY
name: (2s)-amino(cyclopentyl)ethanoic acid
synonyms:
- (2S)-amino(cyclopentyl)ethanoic acid
- (2S)-2-azanyl-2-cyclopentyl-ethanoic acid
identifiers:
- ns: pdb-ccd
id: 2KY
structure: '[NH3+][C@H](C(=O)[O-])C1CCCC1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
2L5:
id: 2L5
name: 2-chloro-l-phenylalanine
synonyms:
- (2S)-2-azanyl-3-(2-chlorophenyl)propanoic acid
- 2-chloro-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: 2L5
structure: '[O-]C(=O)[C@H](Cc1ccccc1Cl)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
2L6:
id: 2L6
name: (3s,6r,8as)-5-oxo-1,2,3,8a-tetrahydrospiro[indolizine-6,2'-pyrrolidine]-3-carboxylic
acid
synonyms:
- (3S,6R,8aS)-5-oxidanylidenespiro[1,2,3,8a-tetrahydroindolizine-6,2'-pyrrolidine]-3-carboxylic
acid
- (3S,6R,8aS)-5-oxo-1,2,3,8a-tetrahydrospiro[indolizine-6,2'-pyrrolidine]-3-carboxylic
acid
identifiers:
- ns: pdb-ccd
id: 2L6
structure: '[O-]C(=O)[C@@H]1CC[C@@H]2N1C(=O)[C@@]1(C=C2)[NH2+]CCC1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
2L9:
id: 2L9
name: (3ar,5as,8s,10as)-10-oxo-1,2,3,3a,5a,8,10,10a-octahydrodipyrrolo[1,2-a:3',2'-e]azepine-8-carboxylic
acid
synonyms:
- (3aR,5aS,8S,10aS)-10-oxidanylidene-2,3,3a,5a,8,10a-hexahydro-1H-dipyrrolo[3,2-b:3',1'-f]azepine-8-carboxylic
acid
- (3aR,5aS,8S,10aS)-10-oxo-1,2,3,3a,5a,8,10,10a-octahydrodipyrrolo[1,2-a:3',2'-e]azepine-8-carboxylic
acid
identifiers:
- ns: pdb-ccd
id: 2L9
structure: '[O-]C(=O)[C@@H]1C=C[C@H]2N1C(=O)[C@H]1[NH2+]CC[C@@H]1C=C2'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
2LT:
id: 2LT
name: 3,5-dichloro-l-tyrosine
synonyms:
- 3,5-dichloro-L-tyrosine
- (2S)-2-azanyl-3-[3,5-bis(chloranyl)-4-oxidanyl-phenyl]propanoic acid
identifiers:
- ns: pdb-ccd
id: 2LT
structure: '[O-]C(=O)[C@H](Cc1cc(Cl)c(c(c1)Cl)[O-])[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
2ML:
id: 2ML
name: 2-methylleucine
synonyms:
- (2S)-2-amino-2,4-dimethyl-pentanoic acid
- 2-methyl-L-leucine
- L
identifiers:
- ns: pdb-ccd
id: 2ML
structure: CC(C[C@@](C(=O)[O-])([NH3+])C)C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
2MT:
id: 2MT
name: (4r)-2,2-dimethyl-1,3-thiazolidine-4-carboxylic acid
synonyms:
- P
- (4R)-2,2-dimethyl-1,3-thiazolidine-4-carboxylic acid
identifiers:
- ns: pdb-ccd
id: 2MT
structure: '[O-]C(=O)[C@@H]1CSC([NH2+]1)(C)C'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
2OR:
id: 2OR
name: amino{[(2r,3r,4s)-4-amino-2,3,5-trihydroxy-5-oxopentyl]amino}methaniminium
synonyms:
- '[azanyl-[[(2R,3R,4S)-4-azanyl-2,3,5-tris(oxidanyl)-5-oxidanylidene-pentyl]amino]methylidene]azanium'
- amino{[(2R,3R,4S)-4-amino-2,3,5-trihydroxy-5-oxopentyl]amino}methaniminium
- R
identifiers:
- ns: pdb-ccd
id: 2OR
structure: O[C@@H]([C@@H]([C@@H](C(=O)[O-])[NH3+])O)CNC(=[NH2+])N
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
2P0:
id: 2P0
name: 1-({[(s)-hydroxy(phosphonooxy)phosphoryl]oxy}acetyl)-l-proline
synonyms:
- 1-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}acetyl)-L-proline
- (2S)-1-[2-[hydroxy(phosphonooxy)phosphoryl]oxyethanoyl]pyrrolidine-2-carboxylic
acid
identifiers:
- ns: pdb-ccd
id: 2P0
structure: '[O-]C(=O)[C@@H]1CCCN1C(=O)COP(=O)(OP(=O)([O-])[O-])[O-]'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
2QD:
id: 2QD
name: (4r)-4-[3-(methylamino)-3-oxopropyl]-l-glutamic acid
synonyms:
- (2S,4R)-2-azanyl-4-[3-(methylamino)-3-oxidanylidene-propyl]pentanedioic acid
- (4R)-4-[3-(methylamino)-3-oxopropyl]-L-glutamic acid
identifiers:
- ns: pdb-ccd
id: 2QD
structure: CNC(=O)CC[C@@H](C(=O)[O-])C[C@@H](C(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
2QZ:
id: 2QZ
name: n,n-dimethyl-l-threonine
synonyms:
- (2S,3R)-2-(dimethylamino)-3-oxidanyl-butanoic acid
- T
- N,N-dimethyl-L-threonine
identifiers:
- ns: pdb-ccd
id: 2QZ
structure: C[NH+]([C@H](C(=O)[O-])[C@H](O)C)C
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
2R3:
id: 2R3
name: (betar)-beta-hydroxy-o-methyl-l-tyrosine
synonyms:
- (2S,3R)-2-azanyl-3-(4-methoxyphenyl)-3-oxidanyl-propanoic acid
- (betaR)-beta-hydroxy-O-methyl-L-tyrosine
- Y
identifiers:
- ns: pdb-ccd
id: 2R3
structure: COc1ccc(cc1)[C@H]([C@@H](C(=O)[O-])[NH3+])O
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
2RX:
id: 2RX
name: o-thiophosphono-l-serine
synonyms:
- O-thiophosphono-L-serine
- (2S)-2-azanyl-3-[oxidanyl(sulfanyl)phosphoryl]oxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: 2RX
structure: '[O-]C(=O)[C@H](COP(=O)(O)[S-])[NH3+]'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
2SO:
id: 2SO
name: 3-{3-[(3r)-3,4-dihydroxybutyl]-1-(8-phenyloctyl)-1h-imidazol-3-ium-5-yl}-l-alanine
synonyms:
- (2S)-2-azanyl-3-[1-[(3R)-3,4-bis(oxidanyl)butyl]-3-(8-phenyloctyl)imidazol-1-ium-4-yl]propanoic
acid
- 3-{3-[(3R)-3,4-dihydroxybutyl]-1-(8-phenyloctyl)-1H-imidazol-3-ium-5-yl}-L-alanine
identifiers:
- ns: pdb-ccd
id: 2SO
structure: OC[C@@H](CC[n+]1cc(n(c1)CCCCCCCCc1ccccc1)C[C@@H](C(=O)[O-])[NH3+])O
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 29
l_bond_atoms:
- molecule: Monomer
element: N
position: 32
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 31
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 32
- molecule: Monomer
element: H
position: 32
charge: 1
2TY:
id: 2TY
name: 2-hydroxy-5-{[(1e)-2-phenylethylidene]amino}-l-tyrosine
synonyms:
- (2S)-2-amino-3-[2,4-dihydroxy-5-(phenethylideneamino)phenyl]propanoic acid
- Y
- 2-hydroxy-5-{[(1E)-2-phenylethylidene]amino}-L-tyrosine
identifiers:
- ns: pdb-ccd
id: 2TY
structure: '[O-]C(=O)[C@H](Cc1cc(/N=C/Cc2ccccc2)c(cc1O)O)[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 24
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 24
- molecule: Monomer
element: H
position: 24
charge: 1
2VA:
id: 2VA
name: 2'-(l-valyl)amino-2'-deoxyadenosine
synonyms:
- V
- (2S)-2-amino-N-[(2R,3R,4S,5R)-2-(6-aminopurin-9-yl)-4-hydroxy-5-(hydroxymethyl)oxolan-3-yl]-3-methyl-butanamide
- 2'-deoxy-2'-(L-valylamino)adenosine
identifiers:
- ns: pdb-ccd
id: 2VA
structure: OC[C@H]1O[C@H]([C@@H]([C@@H]1O)NC(=O)[C@H](C(C)C)[NH3+])n1cnc2c1ncnc2N
base_monomers:
- V
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
2XA:
id: 2XA
name: (2r)-2-amino-3-[(4-chlorophenyl)-diphenyl-methyl]sulfanyl-propanoic acid
synonyms:
- (2R)-2-amino-3-[(4-chlorophenyl)-diphenyl-methyl]sulfanyl-propanoic acid
- C
identifiers:
- ns: pdb-ccd
id: 2XA
structure: Clc1ccc(cc1)C(c1ccccc1)(c1ccccc1)SC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 25
l_bond_atoms:
- molecule: Monomer
element: N
position: 28
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 28
- molecule: Monomer
element: H
position: 28
charge: 1
2YC:
id: 2YC
name: n~6~-{[(2s,3s)-3-methyl-3,4-dihydro-2h-pyrrol-2-yl]carbonyl}-l-lysine
synonyms:
- N~6~-{[(2S,3S)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine
- (2S)-2-azanyl-6-[[(2S,3S)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonylamino]hexanoic
acid
identifiers:
- ns: pdb-ccd
id: 2YC
structure: '[O-]C(=O)[C@H](CCCCNC(=O)[C@H]1N=CC[C@@H]1C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
2YF:
id: 2YF
name: n~6~-[(2r)-2,3,4,5-tetrahydropyridin-2-ylcarbonyl]-l-lysine
synonyms:
- (2S)-2-azanyl-6-[[(2R)-2,3,4,5-tetrahydropyridin-2-yl]carbonylamino]hexanoic
acid
- N~6~-[(2R)-2,3,4,5-tetrahydropyridin-2-ylcarbonyl]-L-lysine
identifiers:
- ns: pdb-ccd
id: 2YF
structure: '[O-]C(=O)[C@@H]([NH3+])CCCCNC(=O)[C@H]1CCCC=N1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
2YG:
id: 2YG
name: n~6~-l-lysyl-l-lysine
synonyms:
- (2S)-2-azanyl-6-[[(2S)-2,6-bis(azanyl)hexanoyl]amino]hexanoic acid
- N~6~-L-lysyl-L-lysine
identifiers:
- ns: pdb-ccd
id: 2YG
structure: '[NH3+]CCCC[C@@H](C(=O)NCCCC[C@@H](C(=O)[O-])[NH3+])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 23
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 23
- molecule: Monomer
element: H
position: 23
charge: 1
2YH:
id: 2YH
name: n~5~-d-ornithyl-l-ornithine
synonyms:
- N~5~-D-ornithyl-L-ornithine
- (2S)-2-azanyl-5-[[(2R)-2,5-bis(azanyl)pentanoyl]amino]pentanoic acid
identifiers:
- ns: pdb-ccd
id: 2YH
structure: '[NH3+]CCC[C@H](C(=O)NCCC[C@@H](C(=O)[O-])[NH3+])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
2YJ:
id: 2YJ
name: n~5~-d-lysyl-l-ornithine
synonyms:
- (2S)-2-azanyl-5-[[(2R)-2,6-bis(azanyl)hexanoyl]amino]pentanoic acid
- N~5~-D-lysyl-L-ornithine
identifiers:
- ns: pdb-ccd
id: 2YJ
structure: '[NH3+]CCCC[C@H](C(=O)NCCC[C@@H](C(=O)[O-])[NH3+])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 19
l_bond_atoms:
- molecule: Monomer
element: N
position: 22
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 21
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 22
- molecule: Monomer
element: H
position: 22
charge: 1
2ZC:
id: 2ZC
name: o-{[4-(2-aminoethyl)phenyl]sulfonyl}-l-serine
synonyms:
- (2S)-2-azanyl-3-[4-(2-azanylethyl)phenyl]sulfonyloxy-propanoic acid
- O-{[4-(2-aminoethyl)phenyl]sulfonyl}-L-serine
identifiers:
- ns: pdb-ccd
id: 2ZC
structure: '[NH3+]CCc1ccc(cc1)S(=O)(=O)OC[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 23
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 23
- molecule: Monomer
element: H
position: 23
charge: 1
30V:
id: 30V
name: s-[(2-carbamoylphenyl)selanyl]-l-cysteine
synonyms:
- (2R)-3-(2-aminocarbonylphenyl)selanylsulfanyl-2-azanyl-propanoic acid
- S-[(2-carbamoylphenyl)selanyl]-L-cysteine
identifiers:
- ns: pdb-ccd
id: 30V
structure: '[NH3+][C@H](C(=O)[O-])CS[Se]c1ccccc1C(=O)N'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
32L:
id: 32L
name: ethyl (3s,4s)-4-amino-3-hydroxy-6-methylheptanoate
synonyms:
- ethyl (3S,4S)-4-amino-3-hydroxy-6-methylheptanoate
- ethyl (3S,4S)-4-azanyl-6-methyl-3-oxidanyl-heptanoate
identifiers:
- ns: pdb-ccd
id: 32L
structure: CCOC(=O)C[C@@H]([C@H](CC(C)C)[NH3+])O
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
32S:
id: 32S
name: (s)-2-amino-3-(4h-selenolo[3,2-b]-pyrrol-6-yl)-propionic acid
synonyms:
- 3-(4H-selenopheno[3,2-b]pyrrol-6-yl)-L-alanine
- (2S)-2-amino-3-(4H-selenopheno[2,3-d]pyrrol-6-yl)propanoic acid
- X
identifiers:
- ns: pdb-ccd
id: 32S
structure: '[O-]C(=O)[C@H](Cc1c[nH]c2c1[se]cc2)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
32T:
id: 32T
name: (s)-2-amino-3-(4h-thieno[3,2-b]-pyrrol-6-yl)-propionic acid
synonyms:
- (2S)-2-amino-3-(4H-thieno[2,3-d]pyrrol-6-yl)propanoic acid
- X
- 3-(4H-thieno[3,2-b]pyrrol-6-yl)-L-alanine
identifiers:
- ns: pdb-ccd
id: 32T
structure: '[O-]C(=O)[C@H](Cc1c[nH]c2c1scc2)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
33S:
id: 33S
name: 3-iodo-l-phenylalanine
synonyms:
- 3-iodo-L-phenylalanine
- (2S)-2-azanyl-3-(3-iodanylphenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: 33S
structure: '[O-]C(=O)[C@H](Cc1cccc(c1)I)[NH3+]'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
33W:
id: 33W
name: 3-(5-bromothiophen-2-yl)-l-alanine
synonyms:
- (2S)-2-azanyl-3-(5-bromanylthiophen-2-yl)propanoic acid
- 3-(5-bromothiophen-2-yl)-L-alanine
identifiers:
- ns: pdb-ccd
id: 33W
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1ccc(s1)Br'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
34E:
id: 34E
name: (3r)-4-[4-(2-methoxyethyl)piperazin-1-yl]-n-methyl-l-valine
synonyms:
- (2S,3R)-4-[4-(2-methoxyethyl)piperazin-1-yl]-3-methyl-2-(methylamino)butanoic
acid
- (3R)-4-[4-(2-methoxyethyl)piperazin-1-yl]-N-methyl-L-valine
identifiers:
- ns: pdb-ccd
id: 34E
structure: COCC[NH+]1CCN(CC1)C[C@H]([C@@H](C(=O)[O-])[NH2+]C)C
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
35Y:
id: 35Y
name: 3-[(1h-tetrazol-5-ylcarbonyl)amino]-l-alanine
synonyms:
- (2S)-2-azanyl-3-(1H-1,2,3,4-tetrazol-5-ylcarbonylamino)propanoic acid
- 3-[(1H-tetrazol-5-ylcarbonyl)amino]-L-alanine
identifiers:
- ns: pdb-ccd
id: 35Y
structure: '[O-]C(=O)[C@H](CNC(=O)c1[n-]nnn1)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
3A5:
id: 3A5
name: (2z,4s)-3-aza-5-carboxyl-2-methyl-4(methylcarboxy)pent-2-enoyl
synonyms:
- (3S)-4-methoxy-4-oxidanylidene-3-[(E)-(1-oxidanyl-1-oxidanylidene-propan-2-ylidene)amino]butanoic
acid
- (3S)-3-[(E)-(1-carboxyethylidene)amino]-4-methoxy-4-oxobutanoic acid (non-preferred
name)
identifiers:
- ns: pdb-ccd
id: 3A5
structure: COC(=O)[C@@H](/N=C(/C(=O)[O-])\C)CC(=O)[O-]
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
3AH:
id: 3AH
name: '[histidin-1-yl-4h-[1,2,4]triazol-5-yl]-amine'
synonyms:
- 1-(3-amino-1H-1,2,4-triazol-5-yl)-L-histidine
- (2S)-2-amino-3-[1-(5-amino-2H-1,2,4-triazol-3-yl)imidazol-4-yl]propanoic acid
- H
identifiers:
- ns: pdb-ccd
id: 3AH
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1cn(cn1)c1nc(n[nH]1)N'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
3AR:
id: 3AR
name: n-omega-propyl-l-arginine
synonyms:
- '{[(4S)-4-amino-4-carboxybutyl]amino}(propylamino)methaniminium'
- X
- '[[[(4S)-4-amino-5-hydroxy-5-oxo-pentyl]amino]-propylamino-methylidene]azanium'
identifiers:
- ns: pdb-ccd
id: 3AR
structure: '[O-]C(=O)[C@@H]([NH3+])CCCNC(=[NH2+])NCCC'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
3BY:
id: 3BY
name: 1-methyl-l-proline
synonyms:
- (2S)-1-methylpyrrolidine-2-carboxylic acid
- 1-methyl-L-proline
identifiers:
- ns: pdb-ccd
id: 3BY
structure: C[NH+]1CCC[C@H]1C(=O)[O-]
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
3CF:
id: 3CF
name: 3-cyano-l-phenylalanine
synonyms:
- F
- 3-cyano-L-phenylalanine
- (2S)-2-azanyl-3-(3-cyanophenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: 3CF
structure: N#Cc1cccc(c1)C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
3CT:
id: 3CT
name: 3-chloro-l-tyrosine
synonyms:
- 3-chloro-L-tyrosine
- (2S)-2-azanyl-3-(3-chloranyl-4-oxidanyl-phenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: 3CT
structure: '[O-]C(=O)[C@H](Cc1ccc(c(c1)Cl)O)[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
3EG:
id: 3EG
name: (2s)-2-amino-4,4,4-trifluorobutanoic acid
synonyms:
- (2S)-2-amino-4,4,4-trifluorobutanoic acid
- (2S)-2-azanyl-4,4,4-tris(fluoranyl)butanoic acid
identifiers:
- ns: pdb-ccd
id: 3EG
structure: '[NH3+][C@H](C(=O)[O-])CC(F)(F)F'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
3FG:
id: 3FG
name: (2s)-amino(3,5-dihydroxyphenyl)ethanoic acid
synonyms:
- (2S)-2-azanyl-2-(3,5-dihydroxyphenyl)ethanoic acid
- (2S)-amino(3,5-dihydroxyphenyl)ethanoic acid
identifiers:
- ns: pdb-ccd
id: 3FG
structure: '[NH3+][C@@H](c1cc(O)cc(c1)O)C(=O)[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
3GA:
id: 3GA
name: (3s)-3-[(2s)-2-amino-3-oxopropyl]piperidine-1-carboximidamide
synonyms:
- A
- (3S)-3-[(2S)-2-amino-3-oxopropyl]piperidine-1-carboximidamide
- (3S)-3-[(2S)-2-azanyl-3-oxo-propyl]piperidine-1-carboximidamide
identifiers:
- ns: pdb-ccd
id: 3GA
structure: '[O-]C(=O)[C@H](C[C@@H]1CCCN(C1)C(=[NH2+])N)[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
3K4:
id: 3K4
name: (2s,3s)-3-methylaziridine-2-carboxylic acid
synonyms:
- (2S,3S)-3-methylaziridine-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: 3K4
structure: '[O-]C(=O)[C@@H]1[C@@H]([NH2+]1)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
3O3:
id: 3O3
name: n-[(3s)-3-amino-3-carboxypropyl]-l-glutamic acid
synonyms:
- N-[(3S)-3-amino-3-carboxypropyl]-L-glutamic acid
- (2S)-2-[[(3S)-3-azanyl-4-hydroxy-4-oxo-butyl]amino]pentanedioic acid
identifiers:
- ns: pdb-ccd
id: 3O3
structure: '[O-]C(=O)CC[C@@H](C(=O)[O-])[NH2+]CC[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
3PM:
id: 3PM
name: o-tert-butyl-d-serine
synonyms:
- (2R)-2-azanyl-3-[(2-methylpropan-2-yl)oxy]propanoic acid
- O-tert-butyl-D-serine
identifiers:
- ns: pdb-ccd
id: 3PM
structure: '[NH3+][C@@H](C(=O)[O-])COC(C)(C)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
3PX:
id: 3PX
name: (3s)-3-(propan-2-yloxy)-l-proline
synonyms:
- (2S,3S)-3-propan-2-yloxypyrrolidine-2-carboxylic acid
- (3S)-3-(propan-2-yloxy)-L-proline
identifiers:
- ns: pdb-ccd
id: 3PX
structure: CC(O[C@H]1CC[NH2+][C@@H]1C(=O)[O-])C
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
3QN:
id: 3QN
name: (e)-n~6~-{2-hydroxy-3-methyl-6-[(phosphonooxy)methyl]benzylidene}-l-lysine
synonyms:
- (2S)-2-azanyl-6-[(E)-[2-hydroxy-3-methyl-6-(phosphonooxymethyl)phenyl]methylideneamino]hexanoic
acid
- K
- (E)-N~6~-{2-hydroxy-3-methyl-6-[(phosphonooxy)methyl]benzylidene}-L-lysine
identifiers:
- ns: pdb-ccd
id: 3QN
structure: '[O-]C(=O)[C@H](CCCC/N=C/c1c(ccc(c1O)C)COP(=O)([O-])[O-])[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 26
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 26
- molecule: Monomer
element: H
position: 26
charge: 1
3TY:
id: 3TY
name: 3-[(3e)-3-(benzylhydrazono)-4-hydroxy-6-oxocyclohexa-1,4-dien-1-yl]-l-alanine
synonyms:
- (2S)-2-amino-3-[(3E)-4-hydroxy-6-oxo-3-(phenylmethylhydrazinylidene)-1-cyclohexa-1,4-dienyl]propanoic
acid
- X
- 3-[(3E)-3-(benzylhydrazono)-4-hydroxy-6-oxocyclohexa-1,4-dien-1-yl]-L-alanine
identifiers:
- ns: pdb-ccd
id: 3TY
structure: '[NH3+][C@H](C(=O)[O-])CC1=C/C(=N\NCc2ccccc2)/C(=CC1=O)[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
3WS:
id: 3WS
name: n,2-dimethyl-l-alanine
synonyms:
- N,2-dimethyl-L-alanine
- 2-methyl-2-(methylamino)propanoic acid
identifiers:
- ns: pdb-ccd
id: 3WS
structure: '[O-]C(=O)C([NH2+]C)(C)C'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
3X9:
id: 3X9
name: 3-{[(1-hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1h-pyrrol-3-yl)methyl]disulfanyl}-l-alanine
synonyms:
- 3-{[(1-hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl]disulfanyl}-L-alanine
- (2R)-2-azanyl-3-[(2,2,5,5-tetramethyl-1-oxidanyl-pyrrol-3-yl)methyldisulfanyl]propanoic
acid
identifiers:
- ns: pdb-ccd
id: 3X9
structure: '[NH3+][C@H](C(=O)[O-])CSSCC1=CC(N(C1(C)C)O)(C)C'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
3XH:
id: 3XH
name: 3-hydroxyhippuric acid
synonyms:
- G
- N-[(3-hydroxyphenyl)carbonyl]glycine
- 2-[(3-hydroxyphenyl)carbonylamino]ethanoic acid
identifiers:
- ns: pdb-ccd
id: 3XH
structure: '[O-]C(=O)CNC(=O)c1cccc(c1)O'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
3YM:
id: 3YM
name: 3-methoxy-l-tyrosine
synonyms:
- (2S)-2-azanyl-3-(3-methoxy-4-oxidanyl-phenyl)propanoic acid
- 3-methoxy-L-tyrosine
identifiers:
- ns: pdb-ccd
id: 3YM
structure: COc1cc(ccc1O)C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
3ZH:
id: 3ZH
name: 11-{4-[(2s)-2-amino-2-carboxyethyl]-3-(8-phenyloctyl)-2,3-dihydro-1h-imidazol-1-yl}undecanoic
acid
synonyms:
- 11-{4-[(2S)-2-amino-2-carboxyethyl]-3-(8-phenyloctyl)-2,3-dihydro-1H-imidazol-1-yl}undecanoic
acid
- 11-[4-[(2S)-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]-3-(8-phenyloctyl)-2H-imidazol-1-yl]undecanoic
acid
identifiers:
- ns: pdb-ccd
id: 3ZH
structure: '[O-]C(=O)CCCCCCCCCCN1C=C(N(C1)CCCCCCCCc1ccccc1)C[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 36
l_bond_atoms:
- molecule: Monomer
element: N
position: 39
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 38
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 39
- molecule: Monomer
element: H
position: 39
charge: 1
3ZL:
id: 3ZL
name: n~6~-[(1z)-4-amino-3-oxopenta-1,4-dien-1-yl]-l-lysine
synonyms:
- N~6~-[(1Z)-4-amino-3-oxopenta-1,4-dien-1-yl]-L-lysine
- (2S)-2-azanyl-6-[[(1Z)-4-azanyl-3-oxidanylidene-penta-1,4-dienyl]amino]hexanoic
acid
identifiers:
- ns: pdb-ccd
id: 3ZL
structure: '[O-]C(=O)[C@H](CCCCN/C=C\C(=O)C(=C)N)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
41H:
id: 41H
name: (betas)-beta-methyl-l-phenylalanine
synonyms:
- (betaS)-beta-methyl-L-phenylalanine
- (2S,3S)-2-azanyl-3-phenyl-butanoic acid
identifiers:
- ns: pdb-ccd
id: 41H
structure: C[C@H]([C@@H](C(=O)[O-])[NH3+])c1ccccc1
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
41Q:
id: 41Q
name: 4-imino-l-homoserine
synonyms:
- 4-imino-L-homoserine
- (2S)-2-azanyl-4-azanylidene-4-oxidanyl-butanoic acid
identifiers:
- ns: pdb-ccd
id: 41Q
structure: '[O-]C(=[NH2+])C[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
'432':
id: '432'
name: o-butanoyl-l-serine
synonyms:
- (2S)-2-azanyl-3-butanoyloxy-propanoic acid
- O-butanoyl-L-serine
identifiers:
- ns: pdb-ccd
id: '432'
structure: '[O-]C(=O)[C@@H]([NH3+])COC(=O)CCC'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
4AF:
id: 4AF
name: 4-acetyl-l-phenylalanine
synonyms:
- (2S)-2-azanyl-3-(4-ethanoylphenyl)propanoic acid
- 4-acetyl-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: 4AF
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)C(=O)C'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
4AK:
id: 4AK
name: n~6~-sulfo-l-lysine
synonyms:
- N~6~-sulfo-L-lysine
- (2S)-2-azanyl-6-(sulfoamino)hexanoic acid
identifiers:
- ns: pdb-ccd
id: 4AK
structure: '[NH3+][C@H](C(=O)[O-])CCCCNS(=O)(=O)[O-]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
4AR:
id: 4AR
name: amino({(4s)-4-amino-6-[(2,6-dimethylbenzoyl)oxy]-5-oxohexyl}amino)methaniminium
synonyms:
- '[azanyl-[[(4S)-4-azanyl-6-(2,6-dimethylphenyl)carbonyloxy-5-oxidanylidene-hexyl]amino]methylidene]azanium'
- amino({(4S)-4-amino-6-[(2,6-dimethylbenzoyl)oxy]-5-oxohexyl}amino)methaniminium
identifiers:
- ns: pdb-ccd
id: 4AR
structure: '[NH3+][C@H](C(=O)COC(=O)c1c(C)cccc1C)CCCNC(=[NH2+])N'
base_monomers:
- R
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
4AW:
id: 4AW
name: 4-azatryptophan
synonyms:
- 3-(1H-pyrrolo[3,2-b]pyridin-3-yl)-L-alanine
- (2S)-2-azanyl-3-(1H-pyrrolo[3,2-b]pyridin-3-yl)propanoic acid
- W
identifiers:
- ns: pdb-ccd
id: 4AW
structure: '[O-]C(=O)[C@H](Cc1c[nH]c2c1nccc2)[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
4CF:
id: 4CF
name: 4-cyano-l-phenylalanine
synonyms:
- F
- (2S)-2-azanyl-3-(4-cyanophenyl)propanoic acid
- 4-cyano-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: 4CF
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)C#N'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
4CY:
id: 4CY
name: nitrilo-l-methionine
synonyms:
- M
- nitrilo-L-methionine
- (2S)-2-azanyl-4-thiocyanato-butanoic acid
identifiers:
- ns: pdb-ccd
id: 4CY
structure: N#CSCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
4D4:
id: 4D4
name: (2s,3r)-2-azanyl-5-carbamimidamido-3-oxidanyl-pentanoic acid
synonyms:
- (2S,3R)-2-azanyl-5-carbamimidamido-3-oxidanyl-pentanoic acid
- (2S,3R)-2-amino-5-carbamimidamido-3-hydroxypentanoic acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: 4D4
structure: O[C@@H]([C@@H](C(=O)[O-])[NH3+])CCNC(=[NH2+])N
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
4DB:
id: 4DB
name: (2s)-2-amino-4-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2h-isoindol-2-yl]butanoic
acid
synonyms:
- (2S)-2-amino-4-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]butanoic
acid
- (2S)-2-azanyl-4-[5-(dimethylamino)-1,3-dioxo-isoindol-2-yl]butanoic acid
identifiers:
- ns: pdb-ccd
id: 4DB
structure: '[NH3+][C@H](C(=O)[O-])CCN1C(=O)c2c(C1=O)cc(cc2)N(C)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
4DP:
id: 4DP
name: 3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2h-isoindol-2-yl]-l-alanine
synonyms:
- (2S)-2-amino-3-(5-dimethylamino-1,3-dioxo-isoindol-2-yl)propanoic acid
- 3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine
- W
identifiers:
- ns: pdb-ccd
id: 4DP
structure: '[O-]C(=O)[C@H](CN1C(=O)c2c(C1=O)ccc(c2)N(C)C)[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
4F3:
id: 4F3
name: '[2-(1-amino-2-hydroxy-propyl)-4-(4-fluoro-1h-indol-3-ylmethyl)-5-hydroxy-imidazol-1-yl]-acetic
acid'
synonyms:
- '{2-[(1R,2S)-1-amino-2-hydroxypropyl]-4-[(4-fluoro-1H-indol-3-yl)methyl]-5-hydroxy-1H-imidazol-1-yl}acetic
acid'
- GYG
- 2-[2-[(1R,2S)-1-amino-2-hydroxy-propyl]-4-[(4-fluoro-1H-indol-3-yl)methyl]-5-hydroxy-imidazol-1-yl]ethanoic
acid
identifiers:
- ns: pdb-ccd
id: 4F3
structure: '[O-]C(=O)Cn1c(O)c(nc1[C@H]([C@@H](O)C)[NH3+])Cc1c[nH]c2c1c(F)ccc2'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
4FB:
id: 4FB
name: (4s)-4-fluoro-l-proline
synonyms:
- P
- (2S,4S)-4-fluoropyrrolidine-2-carboxylic acid
- (4S)-4-fluoro-L-proline
identifiers:
- ns: pdb-ccd
id: 4FB
structure: '[O-]C(=O)[C@@H]1C[C@@H](C[NH2+]1)F'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
4FW:
id: 4FW
name: 4-fluorotryptophane
synonyms:
- (2S)-2-amino-3-(4-fluoro-1H-indol-3-yl)propanoic acid
- 4-fluoro-L-tryptophan
- W
identifiers:
- ns: pdb-ccd
id: 4FW
structure: '[O-]C(=O)[C@H](Cc1c[nH]c2c1c(F)ccc2)[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
4GJ:
id: 4GJ
name: 3-(pyridin-4-yldisulfanyl)-l-alanine
synonyms:
- (2R)-2-azanyl-3-(pyridin-4-yldisulfanyl)propanoic acid
- 3-(pyridin-4-yldisulfanyl)-L-alanine
- C
identifiers:
- ns: pdb-ccd
id: 4GJ
structure: '[O-]C(=O)[C@H](CSSc1ccncc1)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
4HH:
id: 4HH
name: o-[(s)-hydroxy{[(3r)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl]oxy}phosphoryl]-l-serine
synonyms:
- O-[(S)-hydroxy{[(3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl]oxy}phosphoryl]-L-serine
- (2S)-2-azanyl-3-[[(3R)-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-(2-sulfanylethylamino)propyl]amino]butoxy]-oxidanyl-phosphoryl]oxy-propanoic
acid
identifiers:
- ns: pdb-ccd
id: 4HH
structure: SCCNC(=O)CCNC(=O)[C@@H](C(COP(=O)(OC[C@@H](C(=O)[O-])[NH3+])[O-])(C)C)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 23
l_bond_atoms:
- molecule: Monomer
element: N
position: 26
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 26
- molecule: Monomer
element: H
position: 26
charge: 1
4HJ:
id: 4HJ
name: o-[(r)-hydroxy{[(3r)-3-hydroxy-4-{[3-({2-[(2-hydroxybenzoyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-2,2-dimethyl-4-oxobutyl]oxy}phosphoryl]-l-serine
synonyms:
- O-[(R)-hydroxy{[(3R)-3-hydroxy-4-{[3-({2-[(2-hydroxybenzoyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-2,2-dimethyl-4-oxobutyl]oxy}phosphoryl]-L-serine
- (2S)-2-azanyl-3-[[(3R)-4-[[3-[2-(2-hydroxyphenyl)carbonylsulfanylethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butoxy]-oxidanyl-phosphoryl]oxy-propanoic
acid
identifiers:
- ns: pdb-ccd
id: 4HJ
structure: O=C(NCCSC(=O)c1ccccc1O)CCNC(=O)[C@@H](C(COP(=O)(OC[C@@H](C(=O)[O-])[NH3+])[O-])(C)C)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 32
l_bond_atoms:
- molecule: Monomer
element: N
position: 35
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 34
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 35
- molecule: Monomer
element: H
position: 35
charge: 1
4HL:
id: 4HL
name: (6e)-4-[(2s)-2-amino-2-carboxyethyl]-6-[2-(4-hydroxybenzyl)hydraziniumylidene]-3-oxocyclohexa-1,4-dien-1-olate
synonyms:
- (6E)-4-[(2S)-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]-6-[(4-hydroxyphenyl)methylamino]azaniumylidene-3-oxidanylidene-cyclohexa-1,4-dien-1-olate
- (6E)-4-[(2S)-2-amino-2-carboxyethyl]-6-[2-(4-hydroxybenzyl)hydraziniumylidene]-3-oxocyclohexa-1,4-dien-1-olate
identifiers:
- ns: pdb-ccd
id: 4HL
structure: '[NH3+][C@H](C(=O)[O-])CC1=C/C(=N\NCc2ccc(cc2)O)/C(=CC1=O)[O-]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
4HT:
id: 4HT
name: 4-hydroxytryptophan
synonyms:
- (2S)-2-amino-3-(4-hydroxy-1H-indol-3-yl)propanoic acid
- 4-hydroxy-L-tryptophan
- W
identifiers:
- ns: pdb-ccd
id: 4HT
structure: '[O-]C(=O)[C@H](Cc1c[nH]c2c1c(O)ccc2)[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
4II:
id: 4II
name: (2~{s})-2-azanyl-3-(4-azidophenyl)propanoic acid
synonyms:
- F
- (2~{S})-2-azanyl-3-(4-azidophenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: 4II
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)N=[N+]=[N-]'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
4IK:
id: 4IK
name: (2s,5s)-2,6-diamino-5-{[(2r,3s,4r,5r)-5-(6-amino-9h-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}hexanoic
acid
synonyms:
- (2S,5S)-2,6-diamino-5-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}hexanoic
acid (non-preferred name)
- (2S,5S)-5-(aminomethyl)-6-[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-2-azanyl-hexanoic
acid
identifiers:
- ns: pdb-ccd
id: 4IK
structure: '[NH3+]C[C@H](C[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)CC[C@@H](C(=O)[O-])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 34
l_bond_atoms:
- molecule: Monomer
element: N
position: 37
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 36
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 37
- molecule: Monomer
element: H
position: 37
charge: 1
4IN:
id: 4IN
name: 4-amino-l-tryptophan
synonyms:
- 4-amino-L-tryptophan
- (2S)-2-azanyl-3-(4-azanyl-1H-indol-3-yl)propanoic acid
- W
identifiers:
- ns: pdb-ccd
id: 4IN
structure: '[O-]C(=O)[C@H](Cc1c[nH]c2c1c(N)ccc2)[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
4J4:
id: 4J4
name: s-(2-{[(2',4'-difluorobiphenyl-4-yl)methyl]amino}-2-oxoethyl)-l-cysteine
synonyms:
- (2R)-2-azanyl-3-[2-[[4-[2,4-bis(fluoranyl)phenyl]phenyl]methylamino]-2-oxidanylidene-ethyl]sulfanyl-propanoic
acid
- S-(2-{[(2',4'-difluorobiphenyl-4-yl)methyl]amino}-2-oxoethyl)-L-cysteine
identifiers:
- ns: pdb-ccd
id: 4J4
structure: O=C(NCc1ccc(cc1)c1ccc(cc1F)F)CSC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 24
l_bond_atoms:
- molecule: Monomer
element: N
position: 27
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 27
- molecule: Monomer
element: H
position: 27
charge: 1
4J5:
id: 4J5
name: amino{[(3s)-3-amino-3-carboxypropyl]amino}methaniminium
synonyms:
- amino{[(3S)-3-amino-3-carboxypropyl]amino}methaniminium
- '[azanyl-[[(3S)-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]amino]methylidene]azanium'
identifiers:
- ns: pdb-ccd
id: 4J5
structure: '[O-]C(=O)[C@H](CCNC(=[NH2+])N)[NH3+]'
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
4L0:
id: 4L0
name: (4r)-1-acetyl-4-(hexyloxy)-l-proline
synonyms:
- (4R)-1-acetyl-4-(hexyloxy)-L-proline
- (2S,4R)-1-ethanoyl-4-hexoxy-pyrrolidine-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: 4L0
structure: CCCCCCO[C@@H]1C[C@H](N(C1)C(=O)C)C(=O)[O-]
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
4L8:
id: 4L8
name: (2r)-2-(aminomethyl)-4-methylpentanoic acid
synonyms:
- (2R)-2-(aminomethyl)-4-methylpentanoic acid
- (2R)-2-(aminomethyl)-4-methyl-pentanoic acid
identifiers:
- ns: pdb-ccd
id: 4L8
structure: '[NH3+]C[C@H](C(=O)[O-])CC(C)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
4LZ:
id: 4LZ
name: o-[2-(triaza-1,2-dien-2-ium-1-yl)ethyl]-l-tyrosine
synonyms:
- O-[2-(triaza-1,2-dien-2-ium-1-yl)ethyl]-L-tyrosine
- azanylidene-[2-[4-[(2S)-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]phenoxy]ethylimino]azanium
identifiers:
- ns: pdb-ccd
id: 4LZ
structure: '[N-]=[N+]=NCCOc1ccc(cc1)C[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
4M8:
id: 4M8
name: (2s)-2-amino-4-[(s)-hydroxy(methoxy)phosphoryl]butanoic acid
synonyms:
- (2S)-2-azanyl-4-[methoxy(oxidanyl)phosphoryl]butanoic acid
- (2S)-2-amino-4-[(S)-hydroxy(methoxy)phosphoryl]butanoic acid
identifiers:
- ns: pdb-ccd
id: 4M8
structure: COP(=O)(CC[C@@H](C(=O)[O-])[NH3+])[O-]
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
4N7:
id: 4N7
name: 1-[(1z)-3-(4-methylphenyl)-3-oxo-1-phenylprop-1-en-1-yl]-l-proline
synonyms:
- 1-[(1Z)-3-(4-methylphenyl)-3-oxo-1-phenylprop-1-en-1-yl]-L-proline
- (2S)-1-[(Z)-3-(4-methylphenyl)-3-oxidanylidene-1-phenyl-prop-1-enyl]pyrrolidine-2-carboxylic
acid
identifiers:
- ns: pdb-ccd
id: 4N7
structure: '[O-]C(=O)[C@@H]1CCCN1/C(=C\C(=O)c1ccc(cc1)C)/c1ccccc1'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
4N8:
id: 4N8
name: 1-[(furan-2-ylmethyl)carbamothioyl]-l-proline
synonyms:
- 1-[(furan-2-ylmethyl)carbamothioyl]-L-proline
- (2S)-1-(furan-2-ylmethylcarbamothioyl)pyrrolidine-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: 4N8
structure: '[O-]C(=O)[C@@H]1CCCN1C(=S)NCc1ccco1'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
4N9:
id: 4N9
name: 1-[(4-cyanobenzyl)carbamothioyl]-l-proline
synonyms:
- 1-[(4-cyanobenzyl)carbamothioyl]-L-proline
- (2S)-1-[(4-cyanophenyl)methylcarbamothioyl]pyrrolidine-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: 4N9
structure: N#Cc1ccc(cc1)CNC(=S)N1CCC[C@H]1C(=O)[O-]
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 19
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 21
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
4NT:
id: 4NT
name: '[(4z)-2-[(1r,2r)-1-amino-2-hydroxypropyl]-4-(3-chloro-4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic
acid'
synonyms:
- 2-[(4Z)-2-[(1R,2R)-1-azanyl-2-oxidanyl-propyl]-4-[(3-chloranyl-4-oxidanyl-phenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
- '[(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(3-chloro-4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic
acid'
identifiers:
- ns: pdb-ccd
id: 4NT
structure: '[O-]C(=O)CN1C(=O)/C(=C/c2ccc(c(c2)Cl)O)/N=C1[C@H]([C@H](O)C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
4NU:
id: 4NU
name: '{(4z)-2-[(1r,2r)-1-amino-2-hydroxypropyl]-4-[(3,5-dichloro-4-oxocyclohexa-2,5-dien-1-yl)methylidene]-5-oxo-4,5-dihydro-1h-imidazol-1-yl}acetic
acid'
synonyms:
- 2-[(4Z)-2-[(1R,2R)-1-azanyl-2-oxidanyl-propyl]-4-[[3,5-bis(chloranyl)-4-oxidanylidene-cyclohexa-2,5-dien-1-yl]methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
- '{(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(3,5-dichloro-4-oxocyclohexa-2,5-dien-1-yl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid'
identifiers:
- ns: pdb-ccd
id: 4NU
structure: '[O-]C(=O)CN1C(=O)/C(=C/[C-]2C=C(Cl)C(=O)C(=C2)Cl)/N=C1[C@H]([C@H](O)C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
4OU:
id: 4OU
name: 4-(acryloylamino)-l-phenylalanine
synonyms:
- 4-(acryloylamino)-L-phenylalanine
- (2S)-2-azanyl-3-[4-(prop-2-enoylamino)phenyl]propanoic acid
identifiers:
- ns: pdb-ccd
id: 4OU
structure: C=CC(=O)Nc1ccc(cc1)C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
4OV:
id: 4OV
name: (2r)-2-[(1r)-2-[(2s)-2-amino-2-carboxyethoxy]-1-{[(2r)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5-methyl-3,6-dihydro-2h-1,3-thiazine-4-carboxylic
acid
synonyms:
- (2R)-2-[(1R)-2-[(2S)-2-amino-2-carboxyethoxy]-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic
acid
- (2R)-2-[(1R)-2-[(2S)-2-azanyl-3-oxidanyl-3-oxidanylidene-propoxy]-1-[[(2R)-2-azanyl-2-phenyl-ethanoyl]amino]-2-oxidanylidene-ethyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic
acid
identifiers:
- ns: pdb-ccd
id: 4OV
structure: '[NH3+][C@H](C(=O)[O-])COC(=O)[C@H]([C@H]1SCC(=C([NH2+]1)C(=O)[O-])C)NC(=O)[C@@H](c1ccccc1)[NH3+]'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
4PH:
id: 4PH
name: 4-methyl-l-phenylalanine
synonyms:
- F
- (2S)-2-azanyl-3-(4-methylphenyl)propanoic acid
- 4-methyl-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: 4PH
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)C'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
4PQ:
id: 4PQ
name: 5-hydroxy-l-tryptophan
synonyms:
- (2S)-2-azanyl-3-(5-oxidanyl-1H-indol-3-yl)propanoic acid
- 5-hydroxy-L-tryptophan
identifiers:
- ns: pdb-ccd
id: 4PQ
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1c[nH]c2c1cc(O)cc2'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
4QK:
id: 4QK
name: 6-[4-(2-aminoethyl)-1h-1,2,3-triazol-1-yl]-l-norleucine
synonyms:
- (2S)-2-azanyl-6-[4-(2-azanylethyl)-1,2,3-triazol-1-yl]hexanoic acid
- 6-[4-(2-aminoethyl)-1H-1,2,3-triazol-1-yl]-L-norleucine
identifiers:
- ns: pdb-ccd
id: 4QK
structure: '[O-]C(=O)[C@@H]([NH3+])CCCCn1cc(nn1)CC[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
4SJ:
id: 4SJ
name: n,beta,beta-trimethyl-l-phenylalanine
synonyms:
- (2S)-3-methyl-2-(methylamino)-3-phenyl-butanoic acid
- N,beta,beta-trimethyl-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: 4SJ
structure: '[O-]C(=O)[C@H](C(c1ccccc1)(C)C)[NH2+]C'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
4U7:
id: 4U7
name: '[(5s)-5-amino-5-carboxy-6,6-difluorohexyl](trihydroxy)borate(1-)'
synonyms:
- A
- '[(5S)-5-azanyl-5-[bis(fluoranyl)methyl]-6-oxidanyl-6-oxidanylidene-hexyl]-tris(oxidanyl)boranuide'
- '[(5S)-5-amino-5-carboxy-6,6-difluorohexyl](trihydroxy)borate(1-)'
identifiers:
- ns: pdb-ccd
id: 4U7
structure: FC([C@@](C(=O)[O-])(CCCC[B-](O)(O)O)[NH3+])F
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
4UD:
id: 4UD
name: (2s)-amino[(5s)-4,5-dihydro-1,2-oxazol-5-yl]acetic acid
synonyms:
- (2S)-amino[(5S)-4,5-dihydro-1,2-oxazol-5-yl]acetic acid
- (2S)-2-azanyl-2-[(5S)-4,5-dihydro-1,2-oxazol-5-yl]ethanoic acid
identifiers:
- ns: pdb-ccd
id: 4UD
structure: '[O-]C(=O)[C@@H]([NH3+])[C@@H]1CC=NO1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
4WQ:
id: 4WQ
name: (2s)-2-amino-7,7-dimethyloctanoic acid
synonyms:
- (2S)-2-azanyl-7,7-dimethyl-octanoic acid
- (2S)-2-amino-7,7-dimethyloctanoic acid
identifiers:
- ns: pdb-ccd
id: 4WQ
structure: '[O-]C(=O)[C@H](CCCCC(C)(C)C)[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
51T:
id: 51T
name: 2,3,6-trifluoro-l-tyrosine
synonyms:
- 2,3,6-trifluoro-L-tyrosine
- (2S)-2-azanyl-3-[2,3,6-tris(fluoranyl)-4-oxidanyl-phenyl]propanoic acid
identifiers:
- ns: pdb-ccd
id: 51T
structure: '[NH3+][C@H](C(=O)[O-])Cc1c(F)cc(c(c1F)F)[O-]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
'562':
id: '562'
name: n~5~-[n-(2-{2-[2-(triaza-1,2-dien-2-ium-1-yl)ethoxy]ethoxy}ethyl)carbamimidoyl]-l-ornithine
synonyms:
- N~5~-[N-(2-{2-[2-(triaza-1,2-dien-2-ium-1-yl)ethoxy]ethoxy}ethyl)carbamimidoyl]-L-ornithine
- azanylidene-[2-[2-[2-[[N-[(4S)-4-azanyl-5-oxidanyl-5-oxidanylidene-pentyl]carbamimidoyl]amino]ethoxy]ethoxy]ethylimino]azanium
identifiers:
- ns: pdb-ccd
id: '562'
structure: '[N-]=[N+]=NCCOCCOCCNC(=[NH2+])NCCC[C@@H](C(=O)[O-])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 23
l_bond_atoms:
- molecule: Monomer
element: N
position: 26
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 26
- molecule: Monomer
element: H
position: 26
charge: 1
56A:
id: 56A
name: 3-(8-phenyloctyl)-l-histidine
synonyms:
- H
- (2S)-2-azanyl-3-[3-(8-phenyloctyl)imidazol-4-yl]propanoic acid
- 3-(8-phenyloctyl)-L-histidine
identifiers:
- ns: pdb-ccd
id: 56A
structure: '[O-]C(=O)[C@H](Cc1cncn1CCCCCCCCc1ccccc1)[NH3+]'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 26
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 26
- molecule: Monomer
element: H
position: 26
charge: 1
56C:
id: 56C
name: n~5~-{n-[2-(2-{2-[2-(triaza-1,2-dien-2-ium-1-yl)ethoxy]ethoxy}ethoxy)ethyl]carbamimidoyl}-l-ornithine
synonyms:
- N~5~-{N-[2-(2-{2-[2-(triaza-1,2-dien-2-ium-1-yl)ethoxy]ethoxy}ethoxy)ethyl]carbamimidoyl}-L-ornithine
- azanylidene-[2-[2-[2-[2-[[N-[(4S)-4-azanyl-5-oxidanyl-5-oxidanylidene-pentyl]carbamimidoyl]amino]ethoxy]ethoxy]ethoxy]ethylimino]azanium
identifiers:
- ns: pdb-ccd
id: 56C
structure: '[N-]=[N+]=NCCOCCOCCOCCNC(=[NH2+])NCCC[C@@H](C(=O)[O-])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 26
l_bond_atoms:
- molecule: Monomer
element: N
position: 29
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 29
- molecule: Monomer
element: H
position: 29
charge: 1
5AB:
id: 5AB
name: '[(5s)-5-amino-5-carboxyhexyl](trihydroxy)borate'
synonyms:
- A
- '[(5S)-5-amino-5-carboxyhexyl](trihydroxy)borate(1-)'
- '[(5S)-5-azanyl-5-methyl-6-oxidanyl-6-oxidanylidene-hexyl]-tris(oxidanyl)boranuide'
identifiers:
- ns: pdb-ccd
id: 5AB
structure: '[O-]C(=O)[C@](CCCC[B-](O)(O)O)([NH3+])C'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
5CR:
id: 5CR
name: n-acetyl-l-phenylalanine
synonyms:
- F
- (2S)-2-acetamido-3-phenyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: 5CR
structure: '[O-]C(=O)[C@H](Cc1ccccc1)NC(=O)C'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
5CS:
id: 5CS
name: 2-amino-3-(cystein-s-yl)-isoxazolidin-5-yl-acetic acid
synonyms:
- S-{(3R,5R)-5-[(S)-amino(carboxy)methyl]isoxazolidin-3-yl}-L-cysteine
- C
- (2R)-2-amino-3-[[(3R)-5-[(1S)-1-amino-2-hydroxy-2-oxo-ethyl]-1,2-oxazolidin-3-yl]sulfanyl]propanoic
acid
identifiers:
- ns: pdb-ccd
id: 5CS
structure: '[O-]C(=O)[C@H](CS[C@H]1NOC(C1)[C@@H](C(=O)[O-])[NH3+])[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
5CW:
id: 5CW
name: 5-chloro-l-tryptophan
synonyms:
- (2S)-2-azanyl-3-(5-chloranyl-1H-indol-3-yl)propanoic acid
- 5-chloro-L-tryptophan
- W
identifiers:
- ns: pdb-ccd
id: 5CW
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1c[nH]c2c1cc(Cl)cc2'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
5DW:
id: 5DW
name: 4-ethynyl-l-phenylalanine
synonyms:
- 4-ethynyl-L-phenylalanine
- (2S)-2-azanyl-3-(4-ethynylphenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: 5DW
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)C#C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
5FQ:
id: 5FQ
name: n-pentyl-l-alaninamide
synonyms:
- (2S)-2-azanyl-N-pentyl-propanamide
- N-pentyl-L-alaninamide
identifiers:
- ns: pdb-ccd
id: 5FQ
structure: CCCCCNC(=O)[C@@H]([NH3+])C
base_monomers:
- A
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
5GM:
id: 5GM
name: (4s)-2,4-dimethyl-l-norleucine
synonyms:
- (4S)-2,4-dimethyl-L-norleucine
- (2S,4S)-2-azanyl-2,4-dimethyl-hexanoic acid
identifiers:
- ns: pdb-ccd
id: 5GM
structure: CC[C@@H](C[C@@](C(=O)[O-])([NH3+])C)C
base_monomers:
- I
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
5MW:
id: 5MW
name: (2~{s})-5-[4-(aminomethyl)-1,2,3-triazol-1-yl]-2-azanyl-pentanoic acid
synonyms:
- (2~{S})-5-[4-(aminomethyl)-1,2,3-triazol-1-yl]-2-azanyl-pentanoic acid
identifiers:
- ns: pdb-ccd
id: 5MW
structure: '[O-]C(=O)[C@@H]([NH3+])CCCn1cc(nn1)C[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
5OH:
id: 5OH
name: (2s)-amino[(4r,6s)-2-amino-6-hydroxy-3,4,5,6-tetrahydropyrimidin-4-yl]ethanoic
acid
synonyms:
- (2S)-2-azanyl-2-[(4S,6R)-2-azanyl-4-hydroxy-1,4,5,6-tetrahydropyrimidin-6-yl]ethanoic
acid
identifiers:
- ns: pdb-ccd
id: 5OH
structure: '[O-]C(=O)[C@H]([C@H]1C[C@H](O)[NH+]=C(N1)N)N'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
5OL:
id: 5OL
name: n~6~-(1,1-dihydroxyethyl)-l-lysine
synonyms:
- N~6~-(1,1-dihydroxyethyl)-L-lysine
- (2~{S})-2-azanyl-6-[1,1-bis(oxidanyl)ethylamino]hexanoic acid
identifiers:
- ns: pdb-ccd
id: 5OL
structure: '[NH3+][C@H](C(=O)[O-])CCCC[NH2+]C(O)(O)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
5OM:
id: 5OM
name: (2s)-2-amino-8,8-dihydroxy-8-[(2s)-oxiran-2-yl]octanoic acid
synonyms:
- (2S)-2-amino-8,8-dihydroxy-8-[(2S)-oxiran-2-yl]octanoic acid
- (2~{S})-2-azanyl-8,8-bis(oxidanyl)-8-[(2~{S})-oxiran-2-yl]octanoic acid
identifiers:
- ns: pdb-ccd
id: 5OM
structure: '[NH3+][C@H](C(=O)[O-])CCCCCC([C@H]1OC1)(O)O'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
5OW:
id: 5OW
name: (2~{s})-2-azanyl-6-[[(~{z})-~{c}-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-~{n}-[(2~{r})-1-oxidanyl-1-oxidanylidene-3-sulfanyl-propan-2-yl]carbonimidoyl]amino]hexanoic
acid
synonyms:
- (2~{S})-2-azanyl-6-[[(~{Z})-~{C}-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-~{N}-[(2~{R})-1-oxidanyl-1-oxidanylidene-3-sulfanyl-propan-2-yl]carbonimidoyl]amino]hexanoic
acid
- K
identifiers:
- ns: pdb-ccd
id: 5OW
structure: SC[C@@H](C(=O)[O-])/N=C(/c1c(cnc(c1O)C)COP(=O)([O-])[O-])\NCCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
charge: -1
5PG:
id: 5PG
name: (2s)-(4-hydroxyphenyl)(methylamino)ethanoic acid
synonyms:
- (2S)-(4-hydroxyphenyl)(methylamino)ethanoic acid
- (2S)-2-(4-hydroxyphenyl)-2-methylamino-ethanoic acid
identifiers:
- ns: pdb-ccd
id: 5PG
structure: '[O-]C(=O)[C@H](c1ccc(cc1)O)[NH2+]C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
5R5:
id: 5R5
name: methyl (2~{s})-2-azanyl-3-oxidanyl-propanoate
synonyms:
- methyl (2~{S})-2-azanyl-3-oxidanyl-propanoate
identifiers:
- ns: pdb-ccd
id: 5R5
structure: COC(=O)[C@H](CO)N
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
5SQ:
id: 5SQ
name: 2-[2-[(1~{s})-1-azanyl-2-(1~{h}-imidazol-4-yl)ethyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
synonyms:
- 2-[2-[(1~{S})-1-azanyl-2-(1~{H}-imidazol-4-yl)ethyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
- HYG
identifiers:
- ns: pdb-ccd
id: 5SQ
structure: '[O-]C(=O)CN1C(=O)C(=Cc2ccc(cc2)O)N=C1[C@H](Cc1c[nH]cn1)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
5VV:
id: 5VV
name: n-carbamoyl-l-asparagine
synonyms:
- N
- '[(2~{S})-4-azanyl-1,4-bis(oxidanylidene)butan-2-yl]carbamic acid'
identifiers:
- ns: pdb-ccd
id: 5VV
structure: NC(=O)C[C@@H](C(=O)[O-])NC(=O)[O-]
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
5X8:
id: 5X8
name: s-adenosyl-l-cysteine
synonyms:
- (2~{R})-3-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]-2-azanyl-propanoic
acid
identifiers:
- ns: pdb-ccd
id: 5X8
structure: '[O-]C(=O)[C@H](CSC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 30
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 30
- molecule: Monomer
element: H
position: 30
charge: 1
5XU:
id: 5XU
name: (2~{s})-2-azanylpropanal
synonyms:
- (2~{S})-2-azanylpropanal
identifiers:
- ns: pdb-ccd
id: 5XU
structure: '[O-]C(=O)[C@@H]([NH3+])C'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
5ZA:
id: 5ZA
name: (5z)-2-[(1s,2r)-1-amino-2-hydroxypropyl]-5-[(4-amino-1h-indol-3-yl)methylene]-3-(2-hydroxyethyl)-3,5-dihydro-4h-imidazol-4-one
synonyms:
- 2-[(4Z)-2-[(1R,2R)-1-amino-2-hydroxy-propyl]-4-[(4-amino-1H-indol-3-yl)methylidene]-5-oxo-imidazol-1-yl]ethanoic
acid
- '{(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(4-amino-1H-indol-3-yl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid'
- TWG
identifiers:
- ns: pdb-ccd
id: 5ZA
structure: '[O-]C(=O)CN1C(=O)/C(=C/c2c[nH]c3c2c(N)ccc3)/N=C1[C@H]([C@H](O)C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
60F:
id: 60F
name: (2~{r})-2-azanyl-3-[(~{e})-3-(4-hydroxyphenyl)prop-2-enoyl]sulfanyl-propanoic
acid
synonyms:
- (2~{R})-2-azanyl-3-[(~{E})-3-(4-hydroxyphenyl)prop-2-enoyl]sulfanyl-propanoic
acid
identifiers:
- ns: pdb-ccd
id: 60F
structure: '[NH3+][C@H](C(=O)[O-])CSC(=O)/C=C/c1ccc(cc1)O'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
62H:
id: 62H
name: (2s)-3-amino-2-methylpropanoic acid
synonyms:
- (2~{S})-3-azanyl-2-methyl-propanoic acid
- (2S)-3-amino-2-methylpropanoic acid
identifiers:
- ns: pdb-ccd
id: 62H
structure: '[O-]C(=O)[C@H](C[NH3+])C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
66C:
id: 66C
name: 4-[8-(beta-alanyl)-8,9-dihydro-1h-dibenzo[b,f][1,2,3]triazolo[4,5-d]azocin-1-yl]-l-phenylalanine
synonyms:
- 4-[8-(beta-alanyl)-8,9-dihydro-1H-dibenzo[b,f][1,2,3]triazolo[4,5-d]azocin-1-yl]-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: 66C
structure: '[NH3+]CCC(=O)N1Cc2ccccc2c2c(c3c1cccc3)nnn2c1ccc(cc1)C[C@@H](C(=O)[O-])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 37
l_bond_atoms:
- molecule: Monomer
element: N
position: 40
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 39
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 40
- molecule: Monomer
element: H
position: 40
charge: 1
66D:
id: 66D
name: (4r)-2,4-dimethyl-l-norleucine
synonyms:
- (4R)-2,4-dimethyl-L-norleucine
- (2~{S},4~{R})-2-azanyl-2,4-dimethyl-hexanoic acid
identifiers:
- ns: pdb-ccd
id: 66D
structure: CC[C@H](C[C@@](C(=O)[O-])([NH3+])C)C
base_monomers:
- I
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
66E:
id: 66E
name: n-ethyl-l-valine
synonyms:
- (2~{S})-2-(ethylamino)-3-methyl-butanoic acid
- N-ethyl-L-valine
identifiers:
- ns: pdb-ccd
id: 66E
structure: CC[NH2+][C@H](C(=O)[O-])C(C)C
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 3
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 3
- molecule: Monomer
element: H
position: 3
charge: 1
6CL:
id: 6CL
name: 6-carboxylysine
synonyms:
- '[(2R,6S)-6-amino-1,7-dihydroxy-1,7-dioxo-heptan-2-yl]azanium'
- K
- (1R,5S)-5-amino-1,5-dicarboxypentan-1-aminium
identifiers:
- ns: pdb-ccd
id: 6CL
structure: '[NH3+][C@H](C(=O)[O-])CCC[C@H](C(=O)[O-])[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
6CV:
id: 6CV
name: 3-bromo-l-phenylalanine
synonyms:
- (2~{S})-2-azanyl-3-(3-bromophenyl)propanoic acid
- 3-bromo-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: 6CV
structure: '[O-]C(=O)[C@H](Cc1cccc(c1)Br)[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
6DU:
id: 6DU
name: 2-bromo-l-phenylalanine
synonyms:
- (2~{S})-2-azanyl-3-(2-bromophenyl)propanoic acid
- 2-bromo-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: 6DU
structure: '[O-]C(=O)[C@H](Cc1ccccc1Br)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
6FL:
id: 6FL
name: 5,5,5,5',5',5'-hexafluoro-l-leucine
synonyms:
- (2S)-2-azanyl-5,5,5-tris(fluoranyl)-4-(trifluoromethyl)pentanoic acid
- 5,5,5,5',5',5'-hexafluoro-L-leucine
identifiers:
- ns: pdb-ccd
id: 6FL
structure: '[O-]C(=O)[C@H](CC(C(F)(F)F)C(F)(F)F)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
6GL:
id: 6GL
name: 5-(phosphonooxy)-l-norvaline
synonyms:
- A
- (2S)-2-azanyl-5-phosphonooxy-pentanoic acid
- 5-(phosphonooxy)-L-norvaline
identifiers:
- ns: pdb-ccd
id: 6GL
structure: '[O-]C(=O)[C@H](CCCOP(=O)([O-])[O-])[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
6HN:
id: 6HN
name: 6-nitro-l-norleucine
synonyms:
- 6-nitro-L-norleucine
- (2S)-2-amino-6-nitro-hexanoic acid
- K
identifiers:
- ns: pdb-ccd
id: 6HN
structure: '[O-][N+](=O)CCCC[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
6KM:
id: 6KM
name: s-propanoyl-l-cysteine
synonyms:
- (2~{R})-2-azanyl-3-propanoylsulfanyl-propanoic acid
- S-propanoyl-L-cysteine
identifiers:
- ns: pdb-ccd
id: 6KM
structure: '[O-]C(=O)[C@@H]([NH3+])CSC(=O)CC'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
6KY:
id: 6KY
name: (2s)-2-(dimethylamino)-4-(methylselanyl)butanoic acid
synonyms:
- (2~{S})-2-(dimethylamino)-4-methylselanyl-butanoic acid
- (2S)-2-(dimethylamino)-4-(methylselanyl)butanoic acid
identifiers:
- ns: pdb-ccd
id: 6KY
structure: C[Se]CC[C@H]([NH+](C)C)C(=O)[O-]
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
6M6:
id: 6M6
name: s-[(2-phenylethyl)carbamothioyl]-l-cysteine
synonyms:
- (2~{R})-2-azanyl-3-(2-phenylethylcarbamothioylsulfanyl)propanoic acid
- S-[(2-phenylethyl)carbamothioyl]-L-cysteine
identifiers:
- ns: pdb-ccd
id: 6M6
structure: '[NH3+][C@H](C(=O)[O-])CSC(=S)[N-]CCc1ccccc1'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
6RK:
id: 6RK
name: 4-azanylcyclohexane-1-carboxylic acid
synonyms:
- 4-azanylcyclohexane-1-carboxylic acid
identifiers:
- ns: pdb-ccd
id: 6RK
structure: '[NH3+]C1CCC(CC1)C(=O)[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
6V1:
id: 6V1
name: (2~{r})-2-azanyl-3-[(3~{r})-1-ethyl-2,5-bis(oxidanylidene)pyrrolidin-3-yl]sulfanyl-propanoic
acid
synonyms:
- (2~{R})-2-azanyl-3-[(3~{R})-1-ethyl-2,5-bis(oxidanylidene)pyrrolidin-3-yl]sulfanyl-propanoic
acid
- C
identifiers:
- ns: pdb-ccd
id: 6V1
structure: '[O-]C(=O)[C@@H]([NH3+])CS[C@@H]1CC(=O)N(C1=O)CC'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
6WK:
id: 6WK
name: (2~{r})-2-azanyl-3-[[(2~{s},3~{s})-2,3-bis(oxidanyl)-4-sulfanyl-butyl]disulfanyl]propanoic
acid
synonyms:
- (2~{R})-2-azanyl-3-[[(2~{S},3~{S})-2,3-bis(oxidanyl)-4-sulfanyl-butyl]disulfanyl]propanoic
acid
- C
identifiers:
- ns: pdb-ccd
id: 6WK
structure: SC[C@H]([C@@H](CSSC[C@@H](C(=O)[O-])[NH3+])O)O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
6ZS:
id: 6ZS
name: l-isovaline
synonyms:
- (2~{S})-2-azanyl-2-methyl-butanoic acid
identifiers:
- ns: pdb-ccd
id: 6ZS
structure: '[O-]C(=O)[C@@]([NH3+])(CC)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
73C:
id: 73C
name: (2~{s})-2-azanyl-3-butoxy-propanoic acid
synonyms:
- (2~{S})-2-azanyl-3-butoxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: 73C
structure: CCCCOC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
73N:
id: 73N
name: (2~{s})-5-carbamimidamido-2-(carboxyamino)pentanoic acid
synonyms:
- (2~{S})-5-carbamimidamido-2-(carboxyamino)pentanoic acid
- R
identifiers:
- ns: pdb-ccd
id: 73N
structure: '[O-]C(=O)N[C@H](C(=O)[O-])CCCNC(=[NH2+])N'
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
73O:
id: 73O
name: (2~{s})-2-azanyl-4-(4-hydroxyphenyl)butanoic acid
synonyms:
- (2~{S})-2-azanyl-4-(4-hydroxyphenyl)butanoic acid
- Y
identifiers:
- ns: pdb-ccd
id: 73O
structure: '[NH3+][C@H](C(=O)[O-])CCc1ccc(cc1)O'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
73P:
id: 73P
name: (2~{s})-6-azanyl-2-(carboxyamino)hexanoic acid
synonyms:
- (2~{S})-6-azanyl-2-(carboxyamino)hexanoic acid
- K
identifiers:
- ns: pdb-ccd
id: 73P
structure: '[O-]C(=O)[C@@H](NC(=O)[O-])CCCC[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
74P:
id: 74P
name: (e)-n~6~-(1-carboxy-3-oxobutylidene)-l-lysine
synonyms:
- (2~{S})-2-azanyl-6-[(~{E})-[1-oxidanyl-1,4-bis(oxidanylidene)pentan-2-ylidene]amino]hexanoic
acid
- (E)-N~6~-(1-carboxy-3-oxobutylidene)-L-lysine
identifiers:
- ns: pdb-ccd
id: 74P
structure: CC(=O)C/C(=[NH+]\CCCC[C@@H](C(=O)[O-])[NH3+])/C(=O)[O-]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
7C9:
id: 7C9
name: o-methyl-l-serine
synonyms:
- O-methyl-L-serine
- (2~{S})-2-azanyl-3-methoxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: 7C9
structure: '[O-]C(=O)[C@@H]([NH3+])COC'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
7CC:
id: 7CC
name: n,n-diethyl-l-asparagine
synonyms:
- N,N-diethyl-L-asparagine
- (2~{S})-2-azanyl-4-(diethylamino)-4-oxidanylidene-butanoic acid
identifiers:
- ns: pdb-ccd
id: 7CC
structure: CCN(C(=O)C[C@@H](C(=O)[O-])[NH3+])CC
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
7HA:
id: 7HA
name: n-(3-{[2-(4-chlorophenyl)-5-methyl-1,3-oxazol-4-yl]methoxy}benzyl)-n-(methoxycarbonyl)glycine
synonyms:
- 2-[[3-[[2-(4-chlorophenyl)-5-methyl-1,3-oxazol-4-yl]methoxy]phenyl]methyl-methoxycarbonyl-amino]ethanoic
acid
- N-(3-{[2-(4-chlorophenyl)-5-methyl-1,3-oxazol-4-yl]methoxy}benzyl)-N-(methoxycarbonyl)glycine
identifiers:
- ns: pdb-ccd
id: 7HA
structure: COC(=O)N(Cc1cccc(c1)OCc1nc(oc1C)c1ccc(cc1)Cl)CC(=O)[O-]
r_bond_atoms:
- molecule: Monomer
element: C
position: 29
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
r_displaced_atoms:
- molecule: Monomer
element: O
position: 31
charge: -1
7JA:
id: 7JA
name: n-({(1r,2s)-3-oxo-2-[(2z)-pent-2-en-1-yl]cyclopentyl}acetyl)-l-isoleucine
synonyms:
- N-({(1R,2S)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetyl)-L-isoleucine
- (2S,3S)-3-methyl-2-[2-[(1R,2S)-3-oxo-2-[(Z)-pent-2-enyl]cyclopentyl]ethanoylamino]pentanoic
acid
- I
identifiers:
- ns: pdb-ccd
id: 7JA
structure: CC/C=C\C[C@H]1[C@H](CCC1=O)CC(=O)N[C@@H]([C@H](CC)C)C(=O)[O-]
base_monomers:
- I
r_bond_atoms:
- molecule: Monomer
element: C
position: 25
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
r_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
7N8:
id: 7N8
name: 4-borono-l-phenylalanine
synonyms:
- F
- (2~{S})-2-azanyl-3-[4-(dihydroxyboranyl)phenyl]propanoic acid
identifiers:
- ns: pdb-ccd
id: 7N8
structure: OB(c1ccc(cc1)C[C@@H](C(=O)[O-])[NH3+])O
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
81R:
id: 81R
name: (4r)-4,5-disulfanyl-l-norvaline
synonyms:
- (4R)-4,5-disulfanyl-L-norvaline
- (2S,4R)-2-azanyl-4,5-bis(sulfanyl)pentanoic acid
identifiers:
- ns: pdb-ccd
id: 81R
structure: SC[C@@H](C[C@@H](C(=O)[O-])[NH3+])S
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
81S:
id: 81S
name: (4s)-4,5-disulfanyl-l-norvaline
synonyms:
- (4S)-4,5-disulfanyl-L-norvaline
- (2S,4S)-2-azanyl-4,5-bis(sulfanyl)pentanoic acid
identifiers:
- ns: pdb-ccd
id: 81S
structure: SC[C@H](C[C@@H](C(=O)[O-])[NH3+])S
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
'823':
id: '823'
name: n,n-bis(3-sulfanylpropyl)-l-asparagine
synonyms:
- (2S)-2-azanyl-4-[bis(3-sulfanylpropyl)amino]-4-oxidanylidene-butanoic acid
- N,N-bis(3-sulfanylpropyl)-L-asparagine
identifiers:
- ns: pdb-ccd
id: '823'
structure: SCCCN(C(=O)C[C@@H](C(=O)[O-])[NH3+])CCCS
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
85F:
id: 85F
name: (2r)-2-azanyl-3-[(2r)-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-propanoic
acid
synonyms:
- (2~{R})-2-azanyl-3-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-propanoic
acid
identifiers:
- ns: pdb-ccd
id: 85F
structure: '[NH3+][C@H](C(=O)[O-])CSC[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
85G:
id: 85G
name: n-ethyl-l-glutamine
synonyms:
- N-ethyl-L-glutamine
- (2~{S})-2-azanyl-5-(ethylamino)-5-oxidanylidene-pentanoic acid
identifiers:
- ns: pdb-ccd
id: 85G
structure: '[O-]C(=O)[C@@H]([NH3+])CCC(=O)NCC'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
85J:
id: 85J
name: n-propyl-l-glutamine
synonyms:
- N-propyl-L-glutamine
- (2~{S})-2-azanyl-5-oxidanylidene-5-(propylamino)pentanoic acid
identifiers:
- ns: pdb-ccd
id: 85J
structure: '[O-]C(=O)[C@@H]([NH3+])CCC(=O)NCCC'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
8JB:
id: 8JB
name: (2~{r})-2-azanyl-3-[[(5~{s})-5-[(1~{s})-1-azanyl-2-oxidanyl-2-oxidanylidene-ethyl]-4,5-dihydro-1,2-oxazol-3-yl]sulfanyl]propanoic
acid
synonyms:
- (2~{R})-2-azanyl-3-[[(5~{S})-5-[(1~{S})-1-azanyl-2-oxidanyl-2-oxidanylidene-ethyl]-4,5-dihydro-1,2-oxazol-3-yl]sulfanyl]propanoic
acid
- C
identifiers:
- ns: pdb-ccd
id: 8JB
structure: '[O-]C(=O)[C@H](CSC1=NO[C@@H](C1)[C@@H](C(=O)[O-])[NH3+])[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
8LJ:
id: 8LJ
name: (2s)-2,3-dihydro-1h-pyrrole-2-carboxylic acid
synonyms:
- (2S)-2,3-dihydro-1H-pyrrole-2-carboxylic acid
- (2~{S})-2,3-dihydro-1~{H}-pyrrole-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: 8LJ
structure: '[O-]C(=O)[C@@H]1CC=C[NH2+]1'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
8RE:
id: 8RE
name: 3,4-dihydroxylysine
synonyms:
- (2~{S},3~{R},4~{S})-2,6-bis(azanyl)-3,4-bis(oxidanyl)hexanoic acid
- K
identifiers:
- ns: pdb-ccd
id: 8RE
structure: '[NH3+]CC[C@@H]([C@@H]([C@@H](C(=O)[O-])[NH3+])O)O'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
8SP:
id: 8SP
name: o-[(r)-{[(2r)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine
synonyms:
- O-[(R)-{[(2R)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
- (2S)-2-azanyl-3-[[(2R)-2,3-di(octanoyloxy)propoxy]-oxidanyl-phosphoryl]oxy-propanoic
acid
identifiers:
- ns: pdb-ccd
id: 8SP
structure: CCCCCCCC(=O)OC[C@@H](OC(=O)CCCCCCC)COP(=O)(OC[C@@H](C(=O)[O-])[NH3+])[O-]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 32
l_bond_atoms:
- molecule: Monomer
element: N
position: 35
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 34
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 35
- molecule: Monomer
element: H
position: 35
charge: 1
8WY:
id: 8WY
name: 5,5-dihydroxy-l-norleucine
synonyms:
- 5,5-dihydroxy-L-norleucine
- (2~{S})-2-azanyl-5,5-bis(oxidanyl)hexanoic acid
identifiers:
- ns: pdb-ccd
id: 8WY
structure: '[NH3+][C@H](C(=O)[O-])CCC(O)(O)C'
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
8YR:
id: 8YR
name: (2s)-2-azanyl-2-[(3r)-oxolan-3-yl]ethanoic acid
synonyms:
- (2~{S})-2-azanyl-2-[(3~{R})-oxolan-3-yl]ethanoic acid
identifiers:
- ns: pdb-ccd
id: 8YR
structure: '[O-]C(=O)[C@H]([C@@H]1COCC1)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
9DN:
id: 9DN
name: dansyl-l-asparagine
synonyms:
- N
- (2S)-4-amino-2-[(5-dimethylaminonaphthalen-1-yl)sulfonylamino]-4-oxo-butanoic
acid
- N~2~-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-asparagine
identifiers:
- ns: pdb-ccd
id: 9DN
structure: NC(=O)C[C@@H](C(=O)[O-])NS(=O)(=O)c1cccc2c1cccc2N(C)C
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
'9E7':
id: '9E7'
name: n~6~-(sulfanylmethyl)-l-lysine
synonyms:
- N~6~-(sulfanylmethyl)-L-lysine
- (2~{S})-2-azanyl-6-(sulfanylmethylamino)hexanoic acid
identifiers:
- ns: pdb-ccd
id: '9E7'
structure: SC[NH2+]CCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
9EV:
id: 9EV
name: 6-[(2r)-2-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}-5-oxo-1,3-oxazolidin-3-yl]-l-norleucine
synonyms:
- (2~{S})-2-azanyl-6-[(2~{R})-2-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-5-oxidanylidene-1,3-oxazolidin-3-yl]hexanoic
acid
- 6-[(2R)-2-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}-5-oxo-1,3-oxazolidin-3-yl]-L-norleucine
identifiers:
- ns: pdb-ccd
id: 9EV
structure: O=C1CN([C@H](O1)c1c(cnc(c1O)C)COP(=O)([O-])[O-])CCCC[C@@H](C(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 28
l_bond_atoms:
- molecule: Monomer
element: N
position: 31
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 31
- molecule: Monomer
element: H
position: 31
charge: 1
9KK:
id: 9KK
name: n-methyl norleucine
synonyms:
- (2~{S})-2-(methylamino)hexanoic acid
identifiers:
- ns: pdb-ccd
id: 9KK
structure: CCCC[C@@H](C(=O)[O-])[NH2+]C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
9MN:
id: 9MN
name: (2~{s})-2-azanyl-6-(6-bromanylhexanoylamino)hexanoic acid
synonyms:
- (2~{S})-2-azanyl-6-(6-bromanylhexanoylamino)hexanoic acid
identifiers:
- ns: pdb-ccd
id: 9MN
structure: BrCCCCCC(=O)NCCCC[C@@H](C(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
9NE:
id: 9NE
name: dansyl-l-glutamate
synonyms:
- E
- N-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-glutamic acid
- (2S)-2-[(5-dimethylaminonaphthalen-1-yl)sulfonylamino]pentanedioic acid
identifiers:
- ns: pdb-ccd
id: 9NE
structure: '[O-]C(=O)CC[C@@H](C(=O)[O-])NS(=O)(=O)c1cccc2c1cccc2N(C)C'
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
9NF:
id: 9NF
name: dansyl-l-phenylalanine
synonyms:
- F
- N-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-phenylalanine
- (2S)-2-[(5-dimethylaminonaphthalen-1-yl)sulfonylamino]-3-phenyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: 9NF
structure: '[O-]C(=O)[C@@H](NS(=O)(=O)c1cccc2c1cccc2N(C)C)Cc1ccccc1'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
9NR:
id: 9NR
name: dansyl-l-arginine
synonyms:
- (2S)-5-carbamimidamido-2-[(5-dimethylaminonaphthalen-1-yl)sulfonylamino]pentanoic
acid
- R
- N~2~-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-arginine
identifiers:
- ns: pdb-ccd
id: 9NR
structure: '[O-]C(=O)[C@@H](NS(=O)(=O)c1cccc2c1cccc2N(C)C)CCCNC(=[NH2+])N'
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
9NV:
id: 9NV
name: dansyl-l-norvaline
synonyms:
- V
- N-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-norvaline
- (2S)-2-[(5-dimethylaminonaphthalen-1-yl)sulfonylamino]pentanoic acid
identifiers:
- ns: pdb-ccd
id: 9NV
structure: CCC[C@@H](C(=O)[O-])NS(=O)(=O)c1cccc2c1cccc2N(C)C
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
9R1:
id: 9R1
name: (2s)-2-aminooctanedioic acid
synonyms:
- (2S)-2-aminooctanedioic acid
- (2~{S})-2-azanyloctanedioic acid
identifiers:
- ns: pdb-ccd
id: 9R1
structure: '[O-]C(=O)CCCCC[C@@H](C(=O)[O-])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
9R4:
id: 9R4
name: d-gamma-glutamyl-2-methyl-l-alanine
synonyms:
- D-gamma-glutamyl-2-methyl-L-alanine
- (2~{R})-2-azanyl-5-[(2-methyl-1-oxidanyl-1-oxidanylidene-propan-2-yl)amino]-5-oxidanylidene-pentanoic
acid
identifiers:
- ns: pdb-ccd
id: 9R4
structure: O=C(NC(C(=O)[O-])(C)C)CC[C@H](C(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 3
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 3
9R7:
id: 9R7
name: l-gamma-glutamylglycine
synonyms:
- (2~{S})-2-azanyl-5-(2-hydroxy-2-oxoethylamino)-5-oxidanylidene-pentanoic acid
- L-gamma-glutamylglycine
identifiers:
- ns: pdb-ccd
id: 9R7
structure: O=C(CC[C@@H](C(=O)[O-])[NH3+])NCC(=O)[O-]
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
9WV:
id: 9WV
name: beta-alanyl-3-amino-l-alanine
synonyms:
- beta-alanyl-3-amino-L-alanine
- (2~{S})-3-azanyl-2-(3-azanylpropanoylamino)propanoic acid
identifiers:
- ns: pdb-ccd
id: 9WV
structure: '[NH3+]CCC(=O)N[C@H](C(=O)[O-])C[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
A5N:
id: A5N
name: o-carboxy-4-imino-l-homoserine
synonyms:
- N
- O-carboxy-4-imino-L-homoserine
- (2S)-2-amino-4-carboxyoxy-4-imino-butanoic acid
identifiers:
- ns: pdb-ccd
id: A5N
structure: '[O-]C(=O)OC(=N)C[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
A66:
id: A66
name: 2-aminoethyllysine-carbonylmethylene-adenine
synonyms:
- N~2~-(2-aminoethyl)-N~2~-[(6-amino-9H-purin-9-yl)acetyl]-D-lysine
- (2R)-6-amino-2-[2-aminoethyl-[2-(6-aminopurin-9-yl)ethanoyl]amino]hexanoic acid
- X
identifiers:
- ns: pdb-ccd
id: A66
structure: '[NH3+]CCN([C@@H](C(=O)[O-])CCCC[NH3+])C(=O)Cn1cnc2c1ncnc2N'
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
A8E:
id: A8E
name: (2s)-2-amino-4-bromopent-4-enoic acid
synonyms:
- (2S)-2-amino-4-bromopent-4-enoic acid
- (2S)-2-azanyl-4-bromanyl-pent-4-enoic acid
identifiers:
- ns: pdb-ccd
id: A8E
structure: BrC(=C)C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
AA4:
id: AA4
name: 2-amino-5-hydroxypentanoic acid
synonyms:
- A
- (2S)-2-amino-5-hydroxy-pentanoic acid
- 5-hydroxy-L-norvaline
identifiers:
- ns: pdb-ccd
id: AA4
structure: '[O-]C(=O)[C@@H]([NH3+])CCCO'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
AA6:
id: AA6
name: 3-[4,5-dihydroxy-2-2-(2-hydroxyethylamino)-phenyl]-2-methylamino-propionic
acid
synonyms:
- (2S)-3-[4,5-dihydroxy-2-(hydroxymethylamino)phenyl]-2-(methylamino)propanoic
acid
- 3-hydroxy-6-[(hydroxymethyl)amino]-N-methyl-L-tyrosine
identifiers:
- ns: pdb-ccd
id: AA6
structure: OCNc1cc(O)c(cc1C[C@@H](C(=O)[O-])[NH2+]C)O
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
ADD:
id: ADD
name: 2,6,8-trimethyl-3-amino-9-benzyl-9-methoxynonanoic acid
synonyms:
- (2S,3S,8S,9S)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyl-decanoic acid
- X
- (2S,3S,6R,8S,9S)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldecanoic acid
identifiers:
- ns: pdb-ccd
id: ADD
structure: CO[C@H]([C@H](CC(CC[C@@H]([C@@H](C(=O)[O-])C)[NH3+])C)C)Cc1ccccc1
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
AE5:
id: AE5
name: n-[(2s)-2-amino-2-carboxyethyl]-l-glutamic acid
synonyms:
- N-[(2S)-2-amino-2-carboxyethyl]-L-glutamic acid
- (2S)-2-[[(2S)-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]amino]pentanedioic
acid
identifiers:
- ns: pdb-ccd
id: AE5
structure: '[O-]C(=O)CC[C@@H](C(=O)[O-])[NH2+]C[C@@H](C(=O)[O-])N'
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
AEA:
id: AEA
name: (2-amino-2-carbamoyl-ethylsulfanyl)-acetic acid
synonyms:
- 2-[(2S)-2,3-bis(azanyl)-3-oxidanylidene-propyl]sulfanylethanoic acid
- '{[(2S)-2,3-diamino-3-oxopropyl]sulfanyl}acetic acid'
- C
identifiers:
- ns: pdb-ccd
id: AEA
structure: '[O-]C(=O)CSC[C@H](C(=O)N)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
AFA:
id: AFA
name: n-[7-methyl-oct-2,4-dienoyl]asparagine
synonyms:
- N
- N~2~-[(2Z,4E)-7-methylocta-2,4-dienoyl]-L-asparagine
- (2S)-4-amino-2-[[(2Z,4E)-7-methylocta-2,4-dienoyl]amino]-4-oxo-butanoic acid
identifiers:
- ns: pdb-ccd
id: AFA
structure: CC(C/C=C/C=C\C(=O)N[C@H](C(=O)[O-])CC(=O)N)C
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
AGQ:
id: AGQ
name: 3-[(3e)-3-(carbamimidoylhydrazono)-4-hydroxy-6-oxocyclohexa-1,4-dien-1-yl]-l-alanine
synonyms:
- (2S)-2-azanyl-3-[(3E)-3-(carbamimidoylhydrazinylidene)-4-hydroxy-6-oxo-cyclohexa-1,4-dien-1-yl]propanoic
acid
- 3-[(3E)-3-(2-carbamimidoylhydrazinylidene)-4-hydroxy-6-oxocyclohexa-1,4-dien-1-yl]-L-alanine
identifiers:
- ns: pdb-ccd
id: AGQ
structure: '[O-]C(=O)[C@H](CC1=C/C(=N\NC(=[NH2+])N)/C(=CC1=O)[O-])[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 22
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 22
- molecule: Monomer
element: H
position: 22
charge: 1
AGT:
id: AGT
name: s-{(s)-amino[(4-aminobutyl)amino]methyl}-l-cysteine
synonyms:
- S-{(S)-amino[(4-aminobutyl)amino]methyl}-L-cysteine
- C
- (2R)-2-azanyl-3-[(S)-azanyl-(4-azanylbutylamino)methyl]sulfanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: AGT
structure: '[NH3+]CCCCN[C@@H](SC[C@@H](C(=O)[O-])[NH3+])N'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
AHH:
id: AHH
name: amino-hydroxyheptanoic acid
synonyms:
- (2S,3R)-3-amino-2-hydroxyheptanoic acid
- (2S,3R)-3-amino-2-hydroxy-heptanoic acid
- X
identifiers:
- ns: pdb-ccd
id: AHH
structure: '[O-]C(=O)[C@H]([C@H]([NH3+])CCCC)O'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
AHO:
id: AHO
name: n-acetyl-n-hydroxy-l-ornithine
synonyms:
- A
- (2S)-2-amino-5-(ethanoyl-hydroxy-amino)pentanoic acid
- N~5~-acetyl-N~5~-hydroxy-L-ornithine
identifiers:
- ns: pdb-ccd
id: AHO
structure: '[NH3+][C@H](C(=O)[O-])CCCN(C(=O)C)O'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AHP:
id: AHP
name: 2-amino-heptanoic acid
synonyms:
- A
- (2S)-2-aminoheptanoic acid
identifiers:
- ns: pdb-ccd
id: AHP
structure: CCCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
AIB:
id: AIB
name: alpha-aminoisobutyric acid
synonyms:
- A
- 2-methyl-L-alanine
- 2-amino-2-methyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: AIB
structure: '[O-]C(=O)C([NH3+])(C)C'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
AJE:
id: AJE
name: (3s,4r)-4-amino-1-(3-carboxypropanoyl)pyrrolidine-3-carboxylic acid
synonyms:
- (3S,4R)-4-azanyl-1-(4-oxidanyl-4-oxidanylidene-butanoyl)pyrrolidine-3-carboxylic
acid
- (3S,4R)-4-amino-1-(3-carboxypropanoyl)pyrrolidine-3-carboxylic acid
identifiers:
- ns: pdb-ccd
id: AJE
structure: '[O-]C(=O)CCC(=O)N1C[C@@H]([C@H](C1)C(=O)[O-])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
ALC:
id: ALC
name: 2-amino-3-cyclohexyl-propionic acid
synonyms:
- A
- 3-cyclohexyl-L-alanine
- (2S)-2-amino-3-cyclohexyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: ALC
structure: '[NH3+][C@H](C(=O)[O-])CC1CCCCC1'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
ALN:
id: ALN
name: naphthalen-2-yl-3-alanine
synonyms:
- A
- (2S)-2-amino-3-naphthalen-1-yl-propanoic acid
- (2S)-2-amino-3-naphthalen-1-ylpropanoic acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: ALN
structure: '[O-]C(=O)[C@H](Cc1cccc2c1cccc2)[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
ALO:
id: ALO
name: allo-threonine
synonyms:
- (2S,3S)-2-amino-3-hydroxy-butanoic acid
- L-allothreonine
- T
identifiers:
- ns: pdb-ccd
id: ALO
structure: '[O-]C(=O)[C@@H]([NH3+])[C@@H](O)C'
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
ALS:
id: ALS
name: (3s)-3-(sulfooxy)-l-serine
synonyms:
- A
- (2S,3S)-2-azanyl-3-oxidanyl-3-sulfooxy-propanoic acid
- (3S)-3-(sulfooxy)-L-serine
identifiers:
- ns: pdb-ccd
id: ALS
structure: '[O-]C(=O)[C@H]([C@H](OS(=O)(=O)[O-])O)[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
ALT:
id: ALT
name: thioalanine
synonyms:
- A
- (2S)-2-aminopropanethioic O-acid
identifiers:
- ns: pdb-ccd
id: ALT
structure: '[O-]C(=S)[C@@H]([NH3+])C'
base_monomers:
- A
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
AN6:
id: AN6
name: 5'-{[(3s)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine
synonyms:
- (2S)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl-ethyl-amino]-2-azanyl-butanoic
acid
- 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine
identifiers:
- ns: pdb-ccd
id: AN6
structure: CC[NH+](C[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)CC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 31
l_bond_atoms:
- molecule: Monomer
element: N
position: 34
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 33
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 34
- molecule: Monomer
element: H
position: 34
charge: 1
AN8:
id: AN8
name: (2s)-2-aminononanoic acid
synonyms:
- A
- (2S)-2-aminononanoic acid
- (2S)-2-azanylnonanoic acid
identifiers:
- ns: pdb-ccd
id: AN8
structure: CCCCCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
API:
id: API
name: 2,6-diaminopimelic acid
synonyms:
- (2S,6R)-2,6-bis(azanyl)heptanedioic acid
- (2R,6S)-2,6-diaminoheptanedioic acid
- K
identifiers:
- ns: pdb-ccd
id: API
structure: '[NH3+][C@H](C(=O)[O-])CCC[C@H](C(=O)[O-])[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
APK:
id: APK
name: 5'-o-[(s)-{[(5s)-5-amino-6-oxohexyl]amino}(hydroxy)phosphoryl]adenosine
synonyms:
- N-[(5S)-5-amino-6-oxo-hexyl]-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy]phosphonamidic
acid
- K
- 5'-O-[(S)-{[(5S)-5-amino-6-oxohexyl]amino}(hydroxy)phosphoryl]adenosine
identifiers:
- ns: pdb-ccd
id: APK
structure: '[O-]C(=O)[C@H](CCCCNP(=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)[O-])[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 37
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 37
- molecule: Monomer
element: H
position: 37
charge: 1
APM:
id: APM
name: m-amidinophenyl-3-alanine
synonyms:
- 3-carbamimidoyl-L-phenylalanine
- (2S)-2-amino-3-(3-carbamimidoylphenyl)propanoic acid
- X
identifiers:
- ns: pdb-ccd
id: APM
structure: '[O-]C(=O)[C@H](Cc1cccc(c1)C(=[NH2+])N)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
APP:
id: APP
name: 1-acetyl-2-carboxypiperidine
synonyms:
- (2S)-1-ethanoylpiperidine-2-carboxylic acid
- (2S)-1-acetylpiperidine-2-carboxylic acid
- X
identifiers:
- ns: pdb-ccd
id: APP
structure: CC(=O)N1CCCC[C@H]1C(=O)[O-]
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
AR2:
id: AR2
name: arginyl-benzothiazole-6-carboxylic acid
synonyms:
- 2-[(2S)-2-azanyl-5-carbamimidamido-pentanoyl]-1,3-benzothiazole-6-carboxylic
acid
- R
- 2-(L-arginyl)-1,3-benzothiazole-6-carboxylic acid
identifiers:
- ns: pdb-ccd
id: AR2
structure: N[C@H](C(=O)c1nc2c(s1)cc(cc2)C(=O)[O-])CCCNC(=[NH2+])N
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AR4:
id: AR4
name: 2-azanyl-5-[3-fluoranyl-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-5-oxidanylidene-pentanoic
acid
synonyms:
- 2-azanyl-5-[3-fluoranyl-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-5-oxidanylidene-pentanoic
acid
- E
- (2S)-2-amino-5-{[(2R,3S,4R,5R)-3-fluoro-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]oxy}-5-oxopentanoic
acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: AR4
structure: OCC1OC(C(C1O)(O)F)OC(=O)CCC(C(=O)[O-])[NH3+]
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
ARM:
id: ARM
name: deoxy-methyl-arginine
synonyms:
- 1-[(4S)-4-amino-5-oxo-hexyl]guanidine
- 1-[(4S)-4-amino-5-oxohexyl]guanidine
- R
identifiers:
- ns: pdb-ccd
id: ARM
structure: CC(=O)[C@H](CCCNC(=[NH2+])N)[NH3+]
base_monomers:
- R
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
ARV:
id: ARV
name: 5-n-allyl-arginine
synonyms:
- (Z)-[amino-[[(4S)-4-amino-5-hydroxy-5-oxo-pentyl]amino]methylidene]-prop-2-enyl-azanium
- X
- N-[(1Z)-amino{[(4S)-4-amino-4-carboxybutyl]amino}methylidene]prop-2-en-1-aminium
identifiers:
- ns: pdb-ccd
id: ARV
structure: '[O-]C(=O)[C@@H]([NH3+])CCCN/C(=[NH+]\CC=C)/N'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
AS7:
id: AS7
name: n4-(4-cyanobenzyl)-l-asparagine
synonyms:
- (2S)-2-azanyl-4-[(4-cyanophenyl)methylamino]-4-oxidanylidene-butanoic acid
- N-(4-cyanobenzyl)-L-asparagine
identifiers:
- ns: pdb-ccd
id: AS7
structure: '[NH3+][C@H](C(=O)[O-])CC(=O)NCc1ccc(cc1)C#N'
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AS9:
id: AS9
name: n-[hydroxy(methyl)phosphoryl]-l-aspartic acid
synonyms:
- N-[(R)-hydroxy(methyl)phosphoryl]-L-aspartic acid
- (2S)-2-[(hydroxy-methyl-phosphoryl)amino]butanedioic acid
- X
identifiers:
- ns: pdb-ccd
id: AS9
structure: '[O-]C(=O)C[C@@H](C(=O)[O-])NP(=O)(C)[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
ASB:
id: ASB
name: aspartic acid-4-carboxymethyl ester
synonyms:
- D
- (2S)-2-amino-4-(carboxymethyloxy)-4-oxo-butanoic acid
- (2S)-2-amino-4-(carboxymethoxy)-4-oxobutanoic acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: ASB
structure: O=C(C[C@@H](C(=O)[O-])[NH3+])OCC(=O)[O-]
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
ASL:
id: ASL
name: aspartic acid-4-carboxyethyl ester
synonyms:
- D
- 2-azanyl-4-oxidanylidene-4-(1-oxidanyl-1-oxidanylidene-propan-2-yl)oxy-butanoic
acid
- 2-amino-4-(1-carboxyethoxy)-4-oxobutanoic acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: ASL
structure: O=C(CC(C(=O)[O-])[NH3+])OC(C(=O)[O-])C
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
ASM:
id: ASM
name: 2-amino-4-oxo-4(1h-pyrrol-1-yl)butanoic acid
synonyms:
- (2S)-2-amino-4-oxo-4-pyrrol-1-yl-butanoic acid
- X
- (2S)-2-amino-4-oxo-4-(1H-pyrrol-1-yl)butanoic acid
identifiers:
- ns: pdb-ccd
id: ASM
structure: '[NH3+][C@H](C(=O)[O-])CC(=O)n1cccc1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
AVN:
id: AVN
name: (2s)-amino[(5s)-3-chloro-4,5-dihydroisoxazol-5-yl]acetic acid
synonyms:
- (2S)-amino[(5S)-3-chloro-4,5-dihydroisoxazol-5-yl]ethanoic acid
- (2S)-2-amino-2-[(5S)-3-chloro-4,5-dihydro-1,2-oxazol-5-yl]ethanoic acid
- X
identifiers:
- ns: pdb-ccd
id: AVN
structure: '[O-]C(=O)[C@@H]([NH3+])[C@@H]1CC(=NO1)Cl'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
AZH:
id: AZH
name: azidohomoalanine
synonyms:
- A
- '[(3S)-3-amino-4-hydroxy-4-oxo-butyl]imino-imino-azanium'
- 1-[(3S)-3-amino-3-carboxypropyl]triaza-1,2-dien-2-ium
identifiers:
- ns: pdb-ccd
id: AZH
structure: '[N-]=[N+]=NCC[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
AZK:
id: AZK
name: (s)-2-amino-6-azidohexanoic acid
synonyms:
- (2S)-2-amino-6-azidohexan-1-ol
- K
- (2S)-2-amino-6-azido-hexan-1-ol
identifiers:
- ns: pdb-ccd
id: AZK
structure: '[N-]=[N+]=NCCCC[C@@H](CO)[NH3+]'
base_monomers:
- K
l_bond_atoms:
- molecule: Monomer
element: N
position: 3
AZS:
id: AZS
name: o-diazoacetyl-l-serine
synonyms:
- (2S)-2-amino-3-(2-diazoethanoyloxy)propanoic acid
- S
- O-(diazoacetyl)-L-serine
identifiers:
- ns: pdb-ccd
id: AZS
structure: '[O-]C(=O)[C@@H]([NH3+])COC(=O)C=[N+]=N'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
AZY:
id: AZY
name: 3-azido-l-tyrosine
synonyms:
- 3-azido-L-tyrosine
- (2S)-2-amino-3-(3-azido-4-hydroxy-phenyl)propanoic acid
- Y
identifiers:
- ns: pdb-ccd
id: AZY
structure: '[N-]=[N+]=Nc1cc(ccc1O)C[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
B27:
id: B27
name: (2r,3s) 3-amino-4-mercapto-2-butanol
synonyms:
- (2R,3S)-3-amino-4-sulfanylbutan-2-ol
- (2R,3S)-3-amino-4-sulfanyl-butan-2-ol
identifiers:
- ns: pdb-ccd
id: B27
structure: C[C@H]([C@H]([NH3+])CS)O
base_monomers:
- T
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
B2H:
id: B2H
name: chromophore (thr, trp, gly)
synonyms:
- 2-[2-[(1~{R},2~{R})-1-azanyl-2-oxidanyl-propyl]-4-(1~{H}-indol-3-ylmethyl)-5-oxidanyl-imidazol-1-yl]ethanoic
acid
- TWG
identifiers:
- ns: pdb-ccd
id: B2H
structure: '[O-]C(=O)Cn1c(O)c(nc1[C@H]([C@H](O)C)[NH3+])Cc1c[nH]c2c1cccc2'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
B2N:
id: B2N
name: (2s)-4-amino-2-(aminomethyl)-4-oxobutanoic acid
synonyms:
- (2~{S})-2-(aminomethyl)-4-azanyl-4-oxidanylidene-butanoic acid
- (2S)-4-amino-2-(aminomethyl)-4-oxobutanoic acid
identifiers:
- ns: pdb-ccd
id: B2N
structure: '[NH3+]C[C@@H](C(=O)[O-])CC(=O)N'
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
B3A:
id: B3A
name: (3s)-3-aminobutanoic acid
synonyms:
- A
- (3S)-3-aminobutanoic acid
identifiers:
- ns: pdb-ccd
id: B3A
structure: '[O-]C(=O)C[C@@H]([NH3+])C'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
B3E:
id: B3E
name: (3s)-3-aminohexanedioic acid
synonyms:
- E
- (3S)-3-aminohexanedioic acid
identifiers:
- ns: pdb-ccd
id: B3E
structure: '[O-]C(=O)CC[C@@H](CC(=O)[O-])[NH3+]'
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
B3K:
id: B3K
name: (3s)-3,7-diaminoheptanoic acid
synonyms:
- (3S)-3,7-diaminoheptanoic acid
- K
identifiers:
- ns: pdb-ccd
id: B3K
structure: '[NH3+]CCCC[C@@H](CC(=O)[O-])[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
B3L:
id: B3L
name: (3s)-3-amino-5-methylhexanoic acid
synonyms:
- (3S)-3-amino-5-methyl-hexanoic acid
- X
- (3S)-3-amino-5-methylhexanoic acid
identifiers:
- ns: pdb-ccd
id: B3L
structure: CC(C[C@@H](CC(=O)[O-])[NH3+])C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
B3M:
id: B3M
name: (3r)-3-amino-5-(methylsulfanyl)pentanoic acid
synonyms:
- (3R)-3-amino-5-methylsulfanyl-pentanoic acid
- (3R)-3-amino-5-(methylsulfanyl)pentanoic acid
- X
identifiers:
- ns: pdb-ccd
id: B3M
structure: CSCC[C@@H](CC(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
B3Q:
id: B3Q
name: (3s)-3,6-diamino-6-oxohexanoic acid
synonyms:
- (3S)-3,6-diamino-6-oxo-hexanoic acid
- (3S)-3,6-diamino-6-oxohexanoic acid
- X
identifiers:
- ns: pdb-ccd
id: B3Q
structure: NC(=O)CC[C@@H](CC(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
B3T:
id: B3T
name: 3-amino-2,3,5-trideoxy-d-threo-pentonic acid
synonyms:
- (3R,4R)-3-amino-4-hydroxy-pentanoic acid
- 3-amino-2,3,5-trideoxy-D-threo-pentonic acid
- X
identifiers:
- ns: pdb-ccd
id: B3T
structure: '[O-]C(=O)C[C@@H]([NH3+])[C@H](O)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
B3U:
id: B3U
name: 2-amino-l-histidine
synonyms:
- H
- (2S)-2-azanyl-3-(2-azanyl-1H-imidazol-5-yl)propanoic acid
- 2-amino-L-histidine
identifiers:
- ns: pdb-ccd
id: B3U
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1c[nH+]c([nH]1)N'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
B3X:
id: B3X
name: (3s)-3,5-diamino-5-oxopentanoic acid
synonyms:
- N
- (3S)-3,5-diamino-5-oxopentanoic acid
- (3S)-3,5-diamino-5-oxo-pentanoic acid
identifiers:
- ns: pdb-ccd
id: B3X
structure: '[O-]C(=O)C[C@H](CC(=O)N)[NH3+]'
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
B3Y:
id: B3Y
name: (3s)-3-amino-4-(4-hydroxyphenyl)butanoic acid
synonyms:
- Y
- (3S)-3-amino-4-(4-hydroxyphenyl)butanoic acid
identifiers:
- ns: pdb-ccd
id: B3Y
structure: '[NH3+][C@@H](Cc1ccc(cc1)O)CC(=O)[O-]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
B8R:
id: B8R
name: (2s,10r)-2,10-diamino-11-(dimethylamino)-11-oxoundecanoic acid
synonyms:
- (2~{S},10~{R})-2,10-bis(azanyl)-11-(dimethylamino)-11-oxidanylidene-undecanoic
acid
- (2S,10R)-2,10-diamino-11-(dimethylamino)-11-oxoundecanoic acid
identifiers:
- ns: pdb-ccd
id: B8R
structure: '[O-]C(=O)[C@H](CCCCCCC[C@H](C(=O)N(C)C)[NH3+])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 24
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 24
- molecule: Monomer
element: H
position: 24
charge: 1
BB8:
id: BB8
name: (2s,3s)-beta-hydroxy-phenylalanine
synonyms:
- F
- (betaS)-beta-hydroxy-L-phenylalanine
- (2S,3S)-2-amino-3-hydroxy-3-phenyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: BB8
structure: O[C@H]([C@@H](C(=O)[O-])[NH3+])c1ccccc1
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
BBC:
id: BBC
name: 3-[(4-aminobutyl)sulfinyl]-2-iminopropan-1-ol
synonyms:
- (2E)-3-[(S)-(4-aminobutyl)sulfinyl]-2-iminopropan-1-ol
- 3-[(S)-4-aminobutylsulfinyl]-2-imino-propan-1-ol
- C
identifiers:
- ns: pdb-ccd
id: BBC
structure: OCC(=[NH2+])C[S@@](=O)CCCC[NH3+]
base_monomers:
- C
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
BCS:
id: BCS
name: benzylcysteine
synonyms:
- (2R)-2-amino-3-benzylsulfanyl-propanoic acid
- S-benzyl-L-cysteine
- C
identifiers:
- ns: pdb-ccd
id: BCS
structure: '[NH3+][C@H](C(=O)[O-])CSCc1ccccc1'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
BCX:
id: BCX
name: (3r)-3-amino-4-sulfanylbutanoic acid
synonyms:
- (3R)-3-amino-4-sulfanylbutanoic acid
- (3R)-3-azanyl-4-sulfanyl-butanoic acid
identifiers:
- ns: pdb-ccd
id: BCX
structure: '[O-]C(=O)C[C@@H]([NH3+])CS'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
BE2:
id: BE2
name: 2-aminobenzoic acid
synonyms:
- X
- 2-aminobenzoic acid
identifiers:
- ns: pdb-ccd
id: BE2
structure: '[O-]C(=O)c1ccccc1N'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
BF6:
id: BF6
name: '[(4z)-2-(aminomethyl)-4-{[4-(benzenecarbonyl)phenyl]methylidene}-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic
acid'
synonyms:
- 2-[(4~{Z})-2-(aminomethyl)-5-oxidanylidene-4-[[4-(phenylcarbonyl)phenyl]methylidene]imidazol-1-yl]ethanoic
acid
- '[(4Z)-2-(aminomethyl)-4-{[4-(benzenecarbonyl)phenyl]methylidene}-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic
acid'
identifiers:
- ns: pdb-ccd
id: BF6
structure: '[NH3+]CC1=N/C(=C\c2ccc(cc2)C(=O)c2ccccc2)/C(=O)N1CC(=O)[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 28
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
BF9:
id: BF9
name: '[(4z)-2-[(1r,2s)-1-amino-2-hydroxypropyl]-4-{[4-(benzenecarbonyl)phenyl]methylidene}-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic
acid'
synonyms:
- '[(4Z)-2-[(1R,2S)-1-amino-2-hydroxypropyl]-4-{[4-(benzenecarbonyl)phenyl]methylidene}-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic
acid'
- 2-[(4~{Z})-2-[(1~{R},2~{S})-1-azanyl-2-oxidanyl-propyl]-5-oxidanylidene-4-[[4-(phenylcarbonyl)phenyl]methylidene]imidazol-1-yl]ethanoic
acid
identifiers:
- ns: pdb-ccd
id: BF9
structure: '[O-]C(=O)CN1C(=O)/C(=C/c2ccc(cc2)C(=O)c2ccccc2)/N=C1[C@H]([C@@H](O)C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 24
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
BG1:
id: BG1
name: o-[(2s)-2-{methyl[(methylamino)sulfonyl]amino}pentanoyl]-l-serine
synonyms:
- S
- O-{(2S)-2-[methyl(methylsulfamoyl)amino]pentanoyl}-L-serine
- (2S)-2-amino-3-[(2S)-2-(methyl-(methylsulfamoyl)amino)pentanoyl]oxy-propanoic
acid
identifiers:
- ns: pdb-ccd
id: BG1
structure: CCC[C@H](N(S(=O)(=O)NC)C)C(=O)OC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 19
l_bond_atoms:
- molecule: Monomer
element: N
position: 22
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 21
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 22
- molecule: Monomer
element: H
position: 22
charge: 1
BIF:
id: BIF
name: (r)-2-amino-3-(4-phenylcyclohexyl)propanoic acid
synonyms:
- F
- (2S)-2-amino-3-biphenyl-4-ylpropanoic acid (non-preferred name)
- (2S)-2-amino-3-(4-phenylphenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: BIF
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)c1ccccc1'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
BIL:
id: BIL
name: (3r,4s)-3-amino-4-methylhexanoic acid
synonyms:
- (3R,4S)-3-amino-4-methylhexanoic acid
- (3R,4S)-3-amino-4-methyl-hexanoic acid
- X
identifiers:
- ns: pdb-ccd
id: BIL
structure: '[O-]C(=O)C[C@@H]([NH3+])[C@H](CC)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
BIU:
id: BIU
name: 5-bromo-l-isoleucine
synonyms:
- (2S,3S)-2-amino-5-bromo-3-methyl-pentanoic acid
- 5-bromo-L-isoleucine
- I
identifiers:
- ns: pdb-ccd
id: BIU
structure: '[O-]C(=O)[C@@H]([NH3+])[C@H](CCBr)C'
base_monomers:
- I
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
BJH:
id: BJH
name: 1(r)-1-acetamido-2-(3-carboxy-2-hydroxyphenyl)ethyl boronic acid
synonyms:
- 3-[(2R)-2-acetamido-2-(dihydroxyboranyl)ethyl]-2-hydroxy-benzoic acid
- 3-[(2R)-2-(acetylamino)-2-(dihydroxyboranyl)ethyl]-2-hydroxybenzoic acid
- X
identifiers:
- ns: pdb-ccd
id: BJH
structure: CC(=O)N[C@H](B(O)O)Cc1cccc(c1O)C(=O)[O-]
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
BL2:
id: BL2
name: n-(tert-butoxycarbonyl)-l-leucine
synonyms:
- N-(tert-butoxycarbonyl)-L-leucine
- (2S)-4-methyl-2-[(2-methylpropan-2-yl)oxycarbonylamino]pentanoic acid
- L
identifiers:
- ns: pdb-ccd
id: BL2
structure: CC(C[C@@H](C(=O)[O-])NC(=O)OC(C)(C)C)C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
BMT:
id: BMT
name: 4-methyl-4-[(e)-2-butenyl]-4,n-methyl-threonine
synonyms:
- (E,2S,3R,4R)-4-methyl-2-(methylamino)-3-oxidanyl-oct-6-enoic acid
- T
- 4-[(2E)-but-2-en-1-yl]-2,4,5-trideoxy-2-(methylamino)-L-xylonic acid
identifiers:
- ns: pdb-ccd
id: BMT
structure: C/C=C/C[C@H]([C@H]([C@@H](C(=O)[O-])[NH2+]C)O)C
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
BNN:
id: BNN
name: acetyl-p-amidinophenylalanine
synonyms:
- F
- N-acetyl-4-carbamimidoyl-L-phenylalanine
- (2S)-2-acetamido-3-(4-carbamimidoylphenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: BNN
structure: CC(=O)N[C@H](C(=O)[O-])Cc1ccc(cc1)C(=[NH2+])N
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
BP5:
id: BP5
name: 3-(2,2'-bipyridin-5-yl)-l-alanine
synonyms:
- (2S)-2-azanyl-3-(6-pyridin-2-ylpyridin-3-yl)propanoic acid
- 3-(2,2'-bipyridin-5-yl)-L-alanine
identifiers:
- ns: pdb-ccd
id: BP5
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(nc1)c1ccccn1'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
BPE:
id: BPE
name: (2s)-2-amino-3-[(3-aminopropyl)sulfanyl]propan-1-ol
synonyms:
- (2R)-2-amino-3-[(3-aminopropyl)sulfanyl]propan-1-ol
- (2R)-2-amino-3-(3-aminopropylsulfanyl)propan-1-ol
- C
identifiers:
- ns: pdb-ccd
id: BPE
structure: OC[C@H](CSCCC[NH3+])[NH3+]
base_monomers:
- C
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
BSE:
id: BSE
name: beta-3-serine
synonyms:
- S
- (2S)-2-(aminomethyl)-3-hydroxy-propanoic acid
- (2S)-3-amino-2-(hydroxymethyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: BSE
structure: OC[C@@H](C(=O)[O-])C[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
BUC:
id: BUC
name: s,s-butylthiocysteine
synonyms:
- 3-(butyldisulfanyl)-L-alanine
- (2R)-2-amino-3-butyldisulfanyl-propanoic acid
- C
identifiers:
- ns: pdb-ccd
id: BUC
structure: CCCCSSC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
BW5:
id: BW5
name: (2~{s})-3-(1-adamantyl)-2-azanyl-propanoic acid
synonyms:
- (2~{S})-3-(1-adamantyl)-2-azanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: BW5
structure: '[NH3+][C@H](C(=O)[O-])CC12CC3CC(C2)CC(C1)C3'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
BWB:
id: BWB
name: (2~{s})-2-azanyl-3-[(2~{s},5~{r})-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-propanoic
acid
synonyms:
- (2~{S})-2-azanyl-3-[(2~{S},5~{R})-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-propanoic
acid
- S
identifiers:
- ns: pdb-ccd
id: BWB
structure: '[O-]C(=O)[C@@H]([NH3+])CO[C@H]1OC[C@H](C(C1O)O)O'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
BWV:
id: BWV
name: n~5~-(n-butylcarbamimidoyl)-l-ornithine
synonyms:
- (2~{S})-2-azanyl-5-[(~{N}-butylcarbamimidoyl)amino]pentanoic acid
- N~5~-(N-butylcarbamimidoyl)-L-ornithine
identifiers:
- ns: pdb-ccd
id: BWV
structure: CCCCNC(=[NH2+])NCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
BXT:
id: BXT
name: (2~{s})-2-azanyl-3-[ethyl(methyl)carbamoyl]oxy-propanoic acid
synonyms:
- S
- (2~{S})-2-azanyl-3-[ethyl(methyl)carbamoyl]oxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: BXT
structure: '[O-]C(=O)[C@@H]([NH3+])COC(=O)N(CC)C'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
BYR:
id: BYR
name: 3-bromo-l-tyrosine
synonyms:
- (2S)-2-azanyl-3-(3-bromanyl-4-oxidanyl-phenyl)propanoic acid
- 3-bromo-L-tyrosine
identifiers:
- ns: pdb-ccd
id: BYR
structure: '[O-]C(=O)[C@H](Cc1ccc(c(c1)Br)O)[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
BZK:
id: BZK
name: (2s, 4s, 6s)-2-amino-6-hydroxy-4-methyl-8-oxodecanoic acid
synonyms:
- (2~{S},4~{S},6~{S})-2-azanyl-4-methyl-6-oxidanyl-8-oxidanylidene-decanoic acid
identifiers:
- ns: pdb-ccd
id: BZK
structure: CCC(=O)C[C@H](C[C@H](C[C@@H](C(=O)[O-])[NH3+])C)O
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
C12:
id: C12
name: 2-(1-amino-2-hydroxypropyl)-4-(4-hydroxybenzyl)-1-(2-oxoethyl)-1h-imidazol-5-olate
synonyms:
- 2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzyl)-1-(2-oxoethyl)-1H-imidazol-5-olate
- 2-[(1R,2R)-1-amino-2-hydroxy-propyl]-5-[(4-hydroxyphenyl)methyl]-3-(2-oxoethyl)imidazol-4-olate
- TYG
identifiers:
- ns: pdb-ccd
id: C12
structure: '[O-]C(=O)Cn1c(O)c(nc1[C@H]([C@H](O)C)[NH3+])Cc1ccc(cc1)O'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
C1T:
id: C1T
name: s-[(1s,6r)-3,6-dihydroxy-4-methyl-2,5-dioxocyclohex-3-en-1-yl]-l-cysteine
synonyms:
- (2R)-2-azanyl-3-[(1S,6R)-3,6-dihydroxy-4-methyl-2,5-dioxo-cyclohex-3-en-1-yl]sulfanyl-propanoic
acid
identifiers:
- ns: pdb-ccd
id: C1T
structure: '[O-]C(=O)[C@H](CS[C@H]1[C@H](O)C(=O)C(=C(C1=O)[O-])C)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
C1X:
id: C1X
name: (z)-n~6~-[(4r,5s)-5-(2-carboxyethyl)-4-(carboxymethyl)dihydro-2h-thiopyran-3(4h)-ylidene]-l-lysine
synonyms:
- (E)-N~6~-[(4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)dihydro-2H-thiopyran-3(4H)-ylidene]-L-lysine
- (2S)-2-amino-6-[[(4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)thian-3-ylidene]amino]hexanoic
acid
- K
identifiers:
- ns: pdb-ccd
id: C1X
structure: '[O-]C(=O)C[C@@H]1[C@@H](CSC/C/1=N/CCCC[C@@H](C(=O)[O-])[NH3+])CCC(=O)[O-]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 23
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 23
- molecule: Monomer
element: H
position: 23
charge: 1
C22:
id: C22
name: 3-chloro-l-alanine
synonyms:
- A
- (2R)-2-azanyl-3-chloranyl-propanoic acid
- 3-chloro-L-alanine
identifiers:
- ns: pdb-ccd
id: C22
structure: '[O-]C(=O)[C@@H]([NH3+])CCl'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
C3Y:
id: C3Y
name: s-[(1s)-1-hydroxy-1-(hydroxyamino)ethyl]-l-cysteine
synonyms:
- S-[(1S)-1-hydroxy-1-(hydroxyamino)ethyl]-L-cysteine
- (2R)-2-amino-3-[(1S)-1-hydroxy-1-(hydroxyamino)ethyl]sulfanyl-propanoic acid
- C
identifiers:
- ns: pdb-ccd
id: C3Y
structure: '[O-]C(=O)[C@@H]([NH3+])CS[C@@](NO)(O)C'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
C5C:
id: C5C
name: s-cyclopentyl thiocysteine
synonyms:
- 3-(cyclopentyldisulfanyl)-L-alanine
- C
- (2R)-2-amino-3-cyclopentyldisulfanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: C5C
structure: '[NH3+][C@H](C(=O)[O-])CSSC1CCCC1'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
C66:
id: C66
name: 2-aminoethyllysine-carbonylmethylene-cytosine
synonyms:
- N~2~-(2-aminoethyl)-N~2~-[(4-amino-2-oxopyrimidin-1(2H)-yl)acetyl]-D-lysine
- (2R)-6-amino-2-[2-aminoethyl-[2-(4-amino-2-oxo-pyrimidin-1-yl)ethanoyl]amino]hexanoic
acid
- X
identifiers:
- ns: pdb-ccd
id: C66
structure: '[NH3+]CCN([C@@H](C(=O)[O-])CCCC[NH3+])C(=O)Cn1ccc(nc1=O)N'
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
C6C:
id: C6C
name: s-cyclohexyl thiocysteine
synonyms:
- 3-(cyclohexyldisulfanyl)-L-alanine
- (2R)-2-amino-3-cyclohexyldisulfanyl-propanoic acid
- C
identifiers:
- ns: pdb-ccd
id: C6C
structure: '[O-]C(=O)[C@H](CSSC1CCCCC1)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
C99:
id: C99
name: '{(2r)-2-[(1s,2r)-1-amino-2-hydroxypropyl]-2-hydroxy-4,5-dioxoimidazolidin-1-yl}acetic
acid'
synonyms:
- 2-[(2R)-2-[(1S,2R)-1-amino-2-hydroxy-propyl]-2-hydroxy-4,5-dioxo-imidazolidin-1-yl]ethanoic
acid
- '{(2R)-2-[(1S,2R)-1-amino-2-hydroxypropyl]-2-hydroxy-4,5-dioxoimidazolidin-1-yl}acetic
acid'
- TFG
identifiers:
- ns: pdb-ccd
id: C99
structure: '[O-]C(=O)CN1C(=O)C(=O)N[C@]1(O)[C@H]([C@H](O)C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
CAB:
id: CAB
name: 4,4-dihydroxy-5-oxo-l-norvaline
synonyms:
- (2S)-2-azanyl-4,4-dihydroxy-5-oxo-pentanoic acid
- 4,4-dihydroxy-5-oxo-L-norvaline
identifiers:
- ns: pdb-ccd
id: CAB
structure: O=CC(C[C@@H](C(=O)[O-])[NH3+])(O)O
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
CAF:
id: CAF
name: s-dimethylarsinoyl-cysteine
synonyms:
- (2R)-2-amino-3-dimethylarsorylsulfanyl-propanoic acid
- C
- S-(dimethylarsoryl)-L-cysteine
identifiers:
- ns: pdb-ccd
id: CAF
structure: '[O-]C(=O)[C@H](CS[As](=O)(C)C)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
CAS:
id: CAS
name: s-(dimethylarsenic)cysteine
synonyms:
- S-(dimethylarsanyl)-L-cysteine
- C
- (2R)-2-amino-3-dimethylarsanylsulfanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: CAS
structure: '[NH3+][C@H](C(=O)[O-])CS[As](C)C'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
CCS:
id: CCS
name: carboxymethylated cysteine
synonyms:
- (2R)-2-amino-3-(carboxymethylsulfanyl)propanoic acid
- S-(carboxymethyl)-L-cysteine
- C
identifiers:
- ns: pdb-ccd
id: CCS
structure: '[O-]C(=O)CSC[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
CCY:
id: CCY
name: 2-(1-amino-2-mercapto-ethyl)-5-(4-hydroxy-benzyl)-3-(ethanoyl)-3,5-dihydro-imidazol-4-one
synonyms:
- CYG
- 2-[2-[(1R)-1-amino-2-sulfanyl-ethyl]-4-[(4-hydroxyphenyl)methyl]-5-oxo-imidazolidin-1-yl]ethanoic
acid
- '[(2S,4S)-2-[(1R)-1-amino-2-sulfanylethyl]-4-(4-hydroxybenzyl)-5-oxoimidazolidin-1-yl]acetic
acid'
identifiers:
- ns: pdb-ccd
id: CCY
structure: SC[C@@H](C1NC(C(=O)N1CC(=O)[O-])Cc1ccc(cc1)O)[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
CDE:
id: CDE
name: 1,2-dimethyl-propylamine
synonyms:
- (2R)-3-methylbutan-2-amine
- X
identifiers:
- ns: pdb-ccd
id: CDE
structure: C[C@H](C(C)C)[NH3+]
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
CDV:
id: CDV
name: 3-methyl-2-ureido-butyric acid
synonyms:
- N-carbamoyl-D-valine
- X
- (2R)-2-(aminocarbonylamino)-3-methyl-butanoic acid
identifiers:
- ns: pdb-ccd
id: CDV
structure: NC(=O)N[C@@H](C(=O)[O-])C(C)C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
CE7:
id: CE7
name: (3s)-3-amino-4,4,4-trihydroxybutanamide
synonyms:
- (3S)-3-amino-4,4,4-trihydroxybutanamide
- (3~{S})-3-azanyl-4,4,4-tris(oxidanyl)butanamide
identifiers:
- ns: pdb-ccd
id: CE7
structure: '[NH3+][C@H](C(O)(O)O)CC(=O)N'
base_monomers:
- N
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
CFY:
id: CFY
name: '[(4z)-2-{(2r)-2-[(1s)-1-amino-2-phenylethyl]-2-hydroxy-2,5-dihydro-1,3-thiazol-4-yl}-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic
acid'
synonyms:
- '[(4Z)-2-{(2R)-2-[(1S)-1-amino-2-phenylethyl]-2-hydroxy-2,5-dihydro-1,3-thiazol-4-yl}-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic
acid'
- FCYG
- 2-[(4Z)-2-[(2R)-2-[(1S)-1-azanyl-2-phenyl-ethyl]-2-oxidanyl-5H-1,3-thiazol-4-yl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
identifiers:
- ns: pdb-ccd
id: CFY
structure: '[O-]C(=O)CN1C(=N/C(=C\c2ccc(cc2)O)/C1=O)C1=N[C@@](SC1)(O)[C@H](Cc1ccccc1)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
CG6:
id: CG6
name: beta-methyl-cysteine
synonyms:
- (2~{R},3~{R})-2-azanyl-3-sulfanyl-butanoic acid
- C
identifiers:
- ns: pdb-ccd
id: CG6
structure: '[O-]C(=O)[C@@H]([NH3+])[C@H](S)C'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
CGA:
id: CGA
name: carboxymethylated glutamic acid
synonyms:
- E
- 2-amino-5-(carboxymethoxy)-5-oxopentanoic acid (non-preferred name)
- 2-azanyl-5-(2-hydroxy-2-oxoethyloxy)-5-oxidanylidene-pentanoic acid
identifiers:
- ns: pdb-ccd
id: CGA
structure: O=C(CCC(C(=O)[O-])[NH3+])OCC(=O)[O-]
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
CGV:
id: CGV
name: s-[(r)-carboxy(hydroxy)methyl]-l-cysteine
synonyms:
- S-[(R)-carboxy(hydroxy)methyl]-L-cysteine
- (2R)-2-azanyl-3-[(1R)-1,2-bis(oxidanyl)-2-oxidanylidene-ethyl]sulfanyl-propanoic
acid
identifiers:
- ns: pdb-ccd
id: CGV
structure: '[O-]C(=O)[C@@H](SC[C@@H](C(=O)[O-])[NH3+])O'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
CHG:
id: CHG
name: cyclohexyl-glycine
synonyms:
- (2S)-2-amino-2-cyclohexyl-ethanoic acid
- X
- (2S)-amino(cyclohexyl)ethanoic acid
identifiers:
- ns: pdb-ccd
id: CHG
structure: '[NH3+][C@H](C(=O)[O-])C1CCCCC1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
CHP:
id: CHP
name: 3-chloro-4-hydroxyphenylglycine
synonyms:
- G
- (2S)-amino(3-chloro-4-hydroxyphenyl)ethanoic acid
- (2S)-2-amino-2-(3-chloro-4-hydroxy-phenyl)ethanoic acid
identifiers:
- ns: pdb-ccd
id: CHP
structure: '[O-]C(=O)[C@H](c1ccc(c(c1)Cl)O)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
CJO:
id: CJO
name: '[(2r,4r)-2-[(1r,2r)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzyl)-5-oxoimidazolidin-1-yl]acetic
acid'
synonyms:
- 2-[(4R)-2-[(1R,2R)-1-amino-2-hydroxy-propyl]-4-[(4-hydroxyphenyl)methyl]-5-oxo-imidazolidin-1-yl]ethanoic
acid
- GYG
- '[(2R,4R)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzyl)-5-oxoimidazolidin-1-yl]acetic
acid'
identifiers:
- ns: pdb-ccd
id: CJO
structure: '[O-]C(=O)CN1C(=O)[C@H](NC1[C@H]([C@H](O)C)[NH3+])Cc1ccc(cc1)O'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
CLG:
id: CLG
name: 2-amino-6-[2-(2-aminooxy-acetylamino)-acetylamino]-hexanoic acid
synonyms:
- (2S)-2-amino-6-[2-(2-aminooxyethanoylamino)ethanoylamino]hexanoic acid
- K
- N~6~-{N-[(aminooxy)acetyl]glycyl}-L-lysine
identifiers:
- ns: pdb-ccd
id: CLG
structure: NOCC(=O)NCC(=O)NCCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
CLH:
id: CLH
name: 2-amino-6-[2-(2-oxo-acetylamino)-acetylamino]-hexanoic acid
synonyms:
- K
- (2S)-2-amino-6-[2-(oxaldehydoylamino)ethanoylamino]hexanoic acid
- N~6~-[N-(oxoacetyl)glycyl]-L-lysine
identifiers:
- ns: pdb-ccd
id: CLH
structure: O=CC(=O)NCC(=O)NCCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
CLV:
id: CLV
name: '{(2s)-2-[(1s)-1-aminoethyl]-5-oxo-2,5-dihydro-1h-imidazol-1-yl}acetic acid'
synonyms:
- '{(2S)-2-[(1S)-1-aminoethyl]-5-oxo-2,5-dihydro-1H-imidazol-1-yl}acetic acid'
- 2-[2-[(1S)-1-aminoethyl]-5-oxo-2H-imidazol-1-yl]ethanoic acid
- AFG
identifiers:
- ns: pdb-ccd
id: CLV
structure: '[O-]C(=O)CN1C([C@@H]([NH3+])C)N=CC1=O'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
CME:
id: CME
name: s,s-(2-hydroxyethyl)thiocysteine
synonyms:
- (2R)-2-amino-3-(2-hydroxyethyldisulfanyl)propanoic acid
- C
- 3-[(2-hydroxyethyl)disulfanyl]-L-alanine
identifiers:
- ns: pdb-ccd
id: CME
structure: '[O-]C(=O)[C@@H]([NH3+])CSSCCO'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
CML:
id: CML
name: (2s)-2-{[(2r)-2-amino-2-carboxyethyl]sulfanyl}butanedioic acid
synonyms:
- (2S)-2-[(2R)-2-amino-3-hydroxy-3-oxo-propyl]sulfanylbutanedioic acid
- (2S)-2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}butanedioic acid
- C
identifiers:
- ns: pdb-ccd
id: CML
structure: '[O-]C(=O)C[C@@H](C(=O)[O-])SC[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
CPC:
id: CPC
name: 2-methyl-1-methylamino-cyclopropane carboxylic acid
synonyms:
- (1S,2S)-2-methyl-1-(methylamino)cyclopropanecarboxylic acid
- (1S,2S)-2-methyl-1-methylamino-cyclopropane-1-carboxylic acid
- X
identifiers:
- ns: pdb-ccd
id: CPC
structure: C[NH2+][C@]1(C[C@@H]1C)C(=O)[O-]
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
CQ2:
id: CQ2
name: '{(4z)-4-(4-aminobenzylidene)-2-[(1r,2r)-1-amino-2-hydroxypropyl]-5-oxo-4,5-dihydro-1h-imidazol-1-yl}acetic
acid'
synonyms:
- '{(4Z)-4-(4-aminobenzylidene)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid'
- 2-[(4Z)-4-[(4-aminophenyl)methylidene]-2-[(1R,2R)-1-azanyl-2-oxidanyl-propyl]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
identifiers:
- ns: pdb-ccd
id: CQ2
structure: '[NH3+][C@H](C1=N/C(=C\c2ccc(cc2)N)/C(=O)N1CC(=O)[O-])[C@H](O)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 22
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
CR0:
id: CR0
name: '[2-(1-amino-2-hydroxypropyl)-2-hydroxy-4-isobutyl-5-oxo-2,5-dihydro-1h-imidazol-1-yl]acetaldehyde'
synonyms:
- 2-[(2R)-2-[(1S,2R)-1-amino-2-hydroxy-propyl]-2-hydroxy-4-(2-methylpropyl)-5-oxo-imidazol-1-yl]ethanal
- '[(2R)-2-[(1S,2R)-1-amino-2-hydroxypropyl]-2-hydroxy-4-(2-methylpropyl)-5-oxo-2,5-dihydro-1H-imidazol-1-yl]acetaldehyde'
- TLG
identifiers:
- ns: pdb-ccd
id: CR0
structure: '[O-]C(=O)CN1C(=O)C(=N[C@]1(O)[C@H]([C@H](O)C)[NH3+])CC(C)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
CR2:
id: CR2
name: '{(4z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1h-imidazol-1-yl}acetic
acid'
synonyms:
- 2-[(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-imidazol-1-yl]ethanoic
acid
- GYG
- '{(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid'
identifiers:
- ns: pdb-ccd
id: CR2
structure: '[NH3+]CC1=N/C(=C\c2ccc(cc2)O)/C(=O)N1CC(=O)[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 21
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
CR5:
id: CR5
name: (2r)-2-(aminomethyl)-2,4-dihydroxy-5-oxo-3-(2-oxoethyl)-2,5-dihydro-1h-imidazol-3-ium
synonyms:
- G
- (2R)-2-(aminomethyl)-3-(carboxymethyl)-2,4-dihydroxy-5-oxo-2,5-dihydro-1H-imidazol-3-ium
- 2-[(2R)-2-(aminomethyl)-2,5-dihydroxy-4-oxo-3H-imidazol-1-ium-1-yl]ethanoic
acid
identifiers:
- ns: pdb-ccd
id: CR5
structure: '[NH3+]C[C@@]1(O)NC(=O)C(=[N+]1CC(=O)[O-])[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
CR8:
id: CR8
name: 2-[1-amino-2-(1h-imidazol-5-yl)ethyl]-1-(carboxymethyl)-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1h-imidazol-5-olate
synonyms:
- 2-[(1S)-1-amino-2-(3H-imidazol-4-yl)ethyl]-3-(carboxymethyl)-5-[(4-oxo-1-cyclohexa-2,5-dienylidene)methyl]imidazol-4-olate
- 2-[(1S)-1-amino-2-(1H-imidazol-5-yl)ethyl]-1-(carboxymethyl)-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1H-imidazol-5-olate
- HYG
identifiers:
- ns: pdb-ccd
id: CR8
structure: '[O-]C(=O)Cn1c(O)c(nc1[C@H](Cc1cnc[nH]1)[NH3+])C=C1C=CC(=O)C=C1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
CRF:
id: CRF
name: '[(4z)-2-[(1r,2r)-1-amino-2-hydroxypropyl]-4-(1h-indol-3-ylmethylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic
acid'
synonyms:
- 2-[2-[(1R,2R)-1-azanyl-2-hydroxy-propyl]-4-(1H-indol-3-ylmethylidene)-5-oxo-imidazol-1-yl]ethanoic
acid
- TWG
identifiers:
- ns: pdb-ccd
id: CRF
structure: '[O-]C(=O)CN1C(=O)C(=Cc2c[nH]c3c2cccc3)N=C1[C@H]([C@H](O)C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
CRG:
id: CRG
name: '[2-(1-amino-2-hydroxy-propyl)-4-(3h-imidazol-4-ylmethylene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic
acid'
synonyms:
- 2-[(4Z)-2-[(1R,2R)-1-amino-2-hydroxy-propyl]-4-(1H-imidazol-4-ylmethylidene)-5-oxo-imidazol-1-yl]ethanoic
acid
- THG
- '[(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(1H-imidazol-4-ylmethylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic
acid'
identifiers:
- ns: pdb-ccd
id: CRG
structure: '[O-]C(=O)CN1C(=O)/C(=C/c2c[nH]cn2)/N=C1[C@H]([C@H](O)C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
CRO:
id: CRO
name: '{2-[(1r,2r)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl}acetic
acid'
synonyms:
- 2-[(4Z)-2-[(1R,2R)-1-azanyl-2-oxidanyl-propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
- '[(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic
acid'
- TYG
identifiers:
- ns: pdb-ccd
id: CRO
structure: '[O-]C(=O)CN1C(=O)/C(=C/c2ccc(cc2)O)/N=C1[C@H]([C@H](O)C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
CRX:
id: CRX
name: '[2-(1-aminoethyl)-2-hydroxy-4-methylene-5-oxoimidazolidin-1-yl]acetic acid'
synonyms:
- ASG
- 2-[(2R)-2-[(1S)-1-aminoethyl]-2-hydroxy-4-methylidene-5-oxo-imidazolidin-1-yl]ethanoic
acid
- '{(2R)-2-[(1S)-1-aminoethyl]-2-hydroxy-4-methylidene-5-oxoimidazolidin-1-yl}acetic
acid'
identifiers:
- ns: pdb-ccd
id: CRX
structure: '[O-]C(=O)CN1C(=O)C(=C)N[C@]1(O)[C@@H]([NH3+])C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
CS1:
id: CS1
name: s-(2-anilinyl-sulfanyl)-cysteine
synonyms:
- 3-[(2-aminophenyl)disulfanyl]-L-alanine
- (2R)-2-amino-3-(2-aminophenyl)disulfanyl-propanoic acid
- C
identifiers:
- ns: pdb-ccd
id: CS1
structure: '[O-]C(=O)[C@H](CSSc1ccccc1N)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
CS3:
id: CS3
name: s-[3-oxo-3-(2-thienyl)propyl]-l-cysteine
synonyms:
- S-(3-oxo-3-thiophen-2-ylpropyl)-L-cysteine
- C
- (2R)-2-amino-3-(3-oxo-3-thiophen-2-yl-propyl)sulfanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: CS3
structure: '[O-]C(=O)[C@H](CSCCC(=O)c1cccs1)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
CS4:
id: CS4
name: s-[3-(3,4-dichlorophenyl)-3-oxopropyl]-l-cysteine
synonyms:
- (2R)-2-amino-3-[3-(3,4-dichlorophenyl)-3-oxo-propyl]sulfanyl-propanoic acid
- S-[3-(3,4-dichlorophenyl)-3-oxopropyl]-L-cysteine
- C
identifiers:
- ns: pdb-ccd
id: CS4
structure: '[O-]C(=O)[C@H](CSCCC(=O)c1ccc(c(c1)Cl)Cl)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
CSA:
id: CSA
name: s-acetonylcysteine
synonyms:
- S-(2-oxopropyl)-L-cysteine
- C
- (2R)-2-amino-3-(2-oxopropylsulfanyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: CSA
structure: CC(=O)CSC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
CSH:
id: CSH
name: '[2-(2-hydroxy-1-methyl-ethyl)-4-(1h-imidazol-4-ylmethyl)-5-oxo-imidazolidin-1-yl]-acetic
acid'
synonyms:
- SHG
- 2-[2-[(1R)-1-amino-2-hydroxy-ethyl]-4-(1H-imidazol-4-ylmethyl)-5-oxo-imidazolidin-1-yl]ethanoic
acid
- '[(2S,4S)-2-[(1R)-1-amino-2-hydroxyethyl]-4-(1H-imidazol-4-ylmethyl)-5-oxoimidazolidin-1-yl]acetic
acid'
identifiers:
- ns: pdb-ccd
id: CSH
structure: '[O-]C(=O)CN1C(NC(C1=O)Cc1c[nH]cn1)[C@@H]([NH3+])CO'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
CSJ:
id: CSJ
name: s-[(2-aminophenyl)carbonyl]-l-cysteine
synonyms:
- S-[(2-aminophenyl)carbonyl]-L-cysteine
- (2R)-2-amino-3-(2-aminophenyl)carbonylsulfanyl-propanoic acid
- C
identifiers:
- ns: pdb-ccd
id: CSJ
structure: '[O-]C(=O)[C@H](CSC(=O)c1ccccc1N)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
CSK:
id: CSK
name: s-(methylselanyl)-l-cysteine
synonyms:
- S-(methylselanyl)-L-cysteine
- (2R)-2-azanyl-3-methylselanylsulfanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: CSK
structure: '[O-]C(=O)[C@@H]([NH3+])CS[Se]C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
CSR:
id: CSR
name: s-arsonocysteine
synonyms:
- (2R)-2-amino-3-arsonosulfanyl-propanoic acid
- S-arsono-L-cysteine
- C
identifiers:
- ns: pdb-ccd
id: CSR
structure: '[O-]C(=O)[C@H](CS[As](=O)([O-])[O-])[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
CTE:
id: CTE
name: 7-chlorotryptophan
synonyms:
- (2S)-2-azanyl-3-(7-chloro-1H-indol-3-yl)propanoic acid
- 7-chloro-L-tryptophan
- W
identifiers:
- ns: pdb-ccd
id: CTE
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1c[nH]c2c1cccc2Cl'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
CTH:
id: CTH
name: 4-chlorothreonine
synonyms:
- (2S,3S)-2-amino-4-chloro-3-hydroxy-butanoic acid
- 4-chloro-L-threonine
- T
identifiers:
- ns: pdb-ccd
id: CTH
structure: ClC[C@H]([C@@H](C(=O)[O-])[NH3+])O
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
CWD:
id: CWD
name: 3-(5-chloro-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-l-alanine
synonyms:
- (2S)-2-azanyl-3-[5-chloranyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]propanoic
acid
- 3-(5-chloro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine
identifiers:
- ns: pdb-ccd
id: CWD
structure: '[O-]C(=O)[C@H](Cn1cc(Cl)c(=O)[nH]c1=O)[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
CWR:
id: CWR
name: (4-methyl-5-oxo-2,5-dihydro-1h-imidazol-1-yl)acetic acid
synonyms:
- S
- (4-methyl-5-oxo-2,5-dihydro-1H-imidazol-1-yl)acetic acid
- 2-(4-methyl-5-oxo-2H-imidazol-1-yl)ethanoic acid
identifiers:
- ns: pdb-ccd
id: CWR
structure: '[O-]C(=O)CN1CN=C(C1=O)C'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
CY0:
id: CY0
name: s-{3-[(4-anilinoquinazolin-6-yl)amino]-3-oxopropyl}-l-cysteine
synonyms:
- S-(3-oxo-3-{[4-(phenylamino)quinazolin-6-yl]amino}propyl)-L-cysteine
- (2R)-2-amino-3-[3-oxo-3-[(4-phenylazanylquinazolin-6-yl)amino]propyl]sulfanyl-propanoic
acid
- C
identifiers:
- ns: pdb-ccd
id: CY0
structure: O=C(Nc1ccc2c(c1)c(ncn2)Nc1ccccc1)CCSC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 27
l_bond_atoms:
- molecule: Monomer
element: N
position: 30
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 30
- molecule: Monomer
element: H
position: 30
charge: 1
CY1:
id: CY1
name: acetamidomethylcysteine
synonyms:
- (2R)-3-(acetamidomethylsulfanyl)-2-amino-propanoic acid
- C
- S-[(acetylamino)methyl]-L-cysteine
identifiers:
- ns: pdb-ccd
id: CY1
structure: CC(=O)NCSC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
CY4:
id: CY4
name: s-butyryl-cystein
synonyms:
- (2R)-2-amino-3-butanoylsulfanyl-propanoic acid
- C
- S-butanoyl-L-cysteine
identifiers:
- ns: pdb-ccd
id: CY4
structure: '[O-]C(=O)[C@@H]([NH3+])CSC(=O)CCC'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
CYD:
id: CYD
name: 2-amino-6-(cystein-s-yl)-5-oxo-hexanoic acid
synonyms:
- 6-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-5-oxo-L-norleucine
- (2S)-2-amino-6-[(2R)-2-amino-3-hydroxy-3-oxo-propyl]sulfanyl-5-oxo-hexanoic
acid
- C
identifiers:
- ns: pdb-ccd
id: CYD
structure: O=C(CC[C@@H](C(=O)[O-])[NH3+])CSC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
CYF:
id: CYF
name: 5-[2-(2-amino-2-carbamoyl-ethylsulfanyl)-acetylamino]-2-(3,6-dihydroxy-9,9a-dihydro-3h-xanthen-9-yl)-benzoic
acid
synonyms:
- 5-[({[(2R)-2,3-diamino-3-oxopropyl]sulfanyl}acetyl)amino]-2-(3,6-dihydroxy-9H-xanthen-9-yl)benzoic
acid
- C
- 5-[2-[(2R)-2,3-diamino-3-oxo-propyl]sulfanylethanoylamino]-2-(3,6-dihydroxy-9H-xanthen-9-yl)benzoic
acid
identifiers:
- ns: pdb-ccd
id: CYF
structure: O=C(Nc1ccc(c(c1)C(=O)[O-])C1c2ccc(cc2Oc2c1ccc(c2)O)O)CSC[C@@H](C(=O)N)[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 3
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 3
CYG:
id: CYG
name: 2-amino-4-(amino-3-oxo-propylsulfanylcarbonyl)-butyric acid
synonyms:
- (2S)-2-amino-5-[(2R)-2-amino-3-hydroxy-3-oxo-propyl]sulfanyl-5-oxo-pentanoic
acid
- (2S)-2-amino-5-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-5-oxopentanoic acid
- C
identifiers:
- ns: pdb-ccd
id: CYG
structure: O=C(SC[C@@H](C(=O)[O-])[NH3+])CC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
CYJ:
id: CYJ
name: (z)-n~6~-[(4r,5s)-5-(2-carboxyethyl)-4-(carboxymethyl)piperidin-3-ylidene]-l-lysine
synonyms:
- (2S)-2-amino-6-[[(4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)piperidin-3-ylidene]amino]hexanoic
acid
- K
- (E)-N~6~-[(4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)piperidin-3-ylidene]-L-lysine
identifiers:
- ns: pdb-ccd
id: CYJ
structure: '[O-]C(=O)C[C@@H]1[C@@H](C[NH2+]C/C/1=N/CCCC[C@@H](C(=O)[O-])[NH3+])CCC(=O)[O-]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 22
l_bond_atoms:
- molecule: Monomer
element: N
position: 25
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 25
- molecule: Monomer
element: H
position: 25
charge: 1
CYQ:
id: CYQ
name: 2-amino-3-phosphonomethylsulfanyl-propionic acid
synonyms:
- (2R)-2-amino-3-(phosphonomethylsulfanyl)propanoic acid
- S-(phosphonomethyl)-L-cysteine
- C
identifiers:
- ns: pdb-ccd
id: CYQ
structure: '[O-]C(=O)[C@H](CSCP(=O)(O)[O-])[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
CYR:
id: CYR
name: n~5~-[{[(2r)-2-amino-2-carboxyethyl]sulfanyl}(iminio)methyl]-l-ornithinate
synonyms:
- '{[(4S)-4-amino-4-carboxybutyl]amino}{[(2R)-2-amino-2-carboxyethyl]sulfanyl}methaniminium'
- '[[[(4S)-4-amino-5-hydroxy-5-oxo-pentyl]amino]-[(2R)-2-amino-3-hydroxy-3-oxo-propyl]sulfanyl-methylidene]azanium'
- C
identifiers:
- ns: pdb-ccd
id: CYR
structure: '[NH2+]=C(SC[C@@H](C(=O)[O-])[NH3+])NCCC[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
CYW:
id: CYW
name: s-[(2r)-2-hydroxypropanoyl]-l-cysteine
synonyms:
- (2R)-2-azanyl-3-[(2R)-2-hydroxypropanoyl]sulfanyl-propanoic acid
- S-[(2R)-2-hydroxypropanoyl]-L-cysteine
identifiers:
- ns: pdb-ccd
id: CYW
structure: '[O-]C(=O)[C@@H]([NH3+])CSC(=O)[C@H](O)C'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
CZ2:
id: CZ2
name: s-(dihydroxyarsino)cysteine
synonyms:
- S-(dihydroxyarsanyl)-L-cysteine
- C
- (2R)-2-amino-3-dihydroxyarsanylsulfanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: CZ2
structure: '[O-][As](SC[C@@H](C(=O)[O-])[NH3+])O'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
CZO:
id: CZO
name: '[(2r,4s)-2-[(1s,2r)-1-amino-2-hydroxypropyl]-2-hydroxy-4-(4-hydroxybenzyl)-5-oxoimidazolidin-1-yl]acetic
acid'
synonyms:
- '[(2R,4S)-2-[(1S,2R)-1-amino-2-hydroxypropyl]-2-hydroxy-4-(4-hydroxybenzyl)-5-oxoimidazolidin-1-yl]acetic
acid'
- 2-[(2R,4S)-2-[(1S,2R)-1-amino-2-hydroxy-propyl]-2-hydroxy-4-[(4-hydroxyphenyl)methyl]-5-oxo-imidazolidin-1-yl]ethanoic
acid
- GYG
identifiers:
- ns: pdb-ccd
id: CZO
structure: '[O-]C(=O)CN1C(=O)[C@@H](N[C@]1(O)[C@H]([C@H](O)C)[NH3+])Cc1ccc(cc1)O'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
D0Q:
id: D0Q
name: 5-methyl-l-tryptophan
synonyms:
- (2~{S})-2-azanyl-3-(5-methyl-1~{H}-indol-3-yl)propanoic acid
identifiers:
- ns: pdb-ccd
id: D0Q
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1c[nH]c2c1cc(C)cc2'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
D2T:
id: D2T
name: (3r)-3-(methylsulfanyl)-l-aspartic acid
synonyms:
- (3R)-3-(methylsulfanyl)-L-aspartic acid
- (2R,3R)-2-azanyl-3-methylsulfanyl-butanedioic acid
identifiers:
- ns: pdb-ccd
id: D2T
structure: CS[C@H]([C@@H](C(=O)[O-])[NH3+])C(=O)[O-]
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
D4P:
id: D4P
name: (2s)-amino(4-hydroxyphenyl)acetic acid
synonyms:
- (2S)-2-amino-2-(4-hydroxyphenyl)ethanoic acid
- (2S)-amino(4-hydroxyphenyl)ethanoic acid
- X
identifiers:
- ns: pdb-ccd
id: D4P
structure: '[NH3+][C@@H](c1ccc(cc1)O)C(=O)[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
DAB:
id: DAB
name: 2,4-diaminobutyric acid
synonyms:
- A
- (2S)-2,4-diaminobutanoic acid
identifiers:
- ns: pdb-ccd
id: DAB
structure: '[O-]C(=O)[C@@H]([NH3+])CC[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
DBS:
id: DBS
name: 2-(2,3-dihydroxy-benzoylamino)-3-hydroxy-propionic acid
synonyms:
- S
- N-[(2,3-dihydroxyphenyl)carbonyl]-L-serine
- (2S)-2-[(2,3-dihydroxyphenyl)carbonylamino]-3-hydroxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: DBS
structure: OC[C@@H](C(=O)[O-])NC(=O)c1cccc(c1O)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
DBY:
id: DBY
name: 3,5 dibromotyrosine
synonyms:
- Y
- 3,5-dibromo-L-tyrosine
- (2S)-2-amino-3-(3,5-dibromo-4-hydroxy-phenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: DBY
structure: '[O-]C(=O)[C@H](Cc1cc(Br)c(c(c1)Br)[O-])[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
DBZ:
id: DBZ
name: 3-(benzoylamino)-l-alanine
synonyms:
- A
- 3-[(phenylcarbonyl)amino]-L-alanine
- (2S)-2-amino-3-benzamido-propanoic acid
identifiers:
- ns: pdb-ccd
id: DBZ
structure: '[NH3+][C@H](C(=O)[O-])CNC(=O)c1ccccc1'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
DC2:
id: DC2
name: n-acetyl-s-[(1s)-1,2-dichloroethyl]-l-cysteine
synonyms:
- (2R)-2-acetamido-3-[(1S)-1,2-dichloroethyl]sulfanyl-propanoic acid
- N-acetyl-S-[(1S)-1,2-dichloroethyl]-L-cysteine
- C
identifiers:
- ns: pdb-ccd
id: DC2
structure: '[O-]C(=O)[C@@H](NC(=O)C)CS[C@H](CCl)Cl'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
DFI:
id: DFI
name: 2,2-difluorostatine
synonyms:
- (3R,4S)-4-amino-2,2-difluoro-3-hydroxy-6-methylheptanoic acid
- X
- (3R,4S)-4-amino-2,2-difluoro-3-hydroxy-6-methyl-heptanoic acid
identifiers:
- ns: pdb-ccd
id: DFI
structure: CC(C[C@@H]([C@H](C(C(=O)[O-])(F)F)O)[NH3+])C
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
DFO:
id: DFO
name: 2,2-difluoro-3-hydrostatine
synonyms:
- (4S)-4-amino-2,2-difluoro-3,3-dihydroxy-6-methyl-heptanoic acid
- (4S)-4-amino-2,2-difluoro-3,3-dihydroxy-6-methylheptanoic acid
- X
identifiers:
- ns: pdb-ccd
id: DFO
structure: '[NH3+][C@H](C(C(C(=O)[O-])(F)F)(O)O)CC(C)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
DHL:
id: DHL
name: 2-amino-ethanethiol
synonyms:
- 2-aminoethanethiol
- X
identifiers:
- ns: pdb-ccd
id: DHL
structure: SCC[NH3+]
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
- molecule: Monomer
element: H
position: 4
charge: 1
DHP:
id: DHP
name: 3-decyl-2,5-dioxo-4-hydroxy-3-pyrroline
synonyms:
- 3-decyl-4-hydroxy-1H-pyrrole-2,5-dione
- 3-decyl-4-hydroxy-pyrrole-2,5-dione
- X
identifiers:
- ns: pdb-ccd
id: DHP
structure: CCCCCCCCCCC1=C([O-])C(=O)NC1=O
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
DI7:
id: DI7
name: 2,6-dimethyl-l-tyrosine
synonyms:
- (2S)-2-azanyl-3-(2,6-dimethyl-4-oxidanyl-phenyl)propanoic acid
- Y
- 2,6-dimethyl-L-tyrosine
identifiers:
- ns: pdb-ccd
id: DI7
structure: '[NH3+][C@H](C(=O)[O-])Cc1c(C)cc(cc1C)O'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
DI8:
id: DI8
name: (3s)-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid
synonyms:
- (3S)-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid
identifiers:
- ns: pdb-ccd
id: DI8
structure: '[O-]C(=O)[C@H]1[NH2+]Cc2c(C1)cccc2'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
DIR:
id: DIR
name: 3-{[(e)-amino(hydroxyimino)methyl]amino}alanine
synonyms:
- 3-(N''-hydroxycarbamimidamido)-L-alanine
- R
- (2S)-2-amino-3-[(N'-hydroxycarbamimidoyl)amino]propanoic acid
identifiers:
- ns: pdb-ccd
id: DIR
structure: O/[NH+]=C(/NC[C@@H](C(=O)[O-])N)\N
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
DLS:
id: DLS
name: di-acetyl-lysine
synonyms:
- (2S)-2,6-diacetamidohexanoic acid
- K
- N~2~,N~6~-diacetyl-L-lysine
identifiers:
- ns: pdb-ccd
id: DLS
structure: CC(=O)NCCCC[C@@H](C(=O)[O-])NC(=O)C
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
DM0:
id: DM0
name: n~2~,n~2~,n~6~,n~6~-tetramethyl-l-lysine
synonyms:
- N~2~,N~2~,N~6~,N~6~-tetramethyl-L-lysine
- K
- (2S)-2,6-bis(dimethylamino)hexanoic acid
identifiers:
- ns: pdb-ccd
id: DM0
structure: C[NH+](CCCC[C@@H](C(=O)[O-])[NH+](C)C)C
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
DMK:
id: DMK
name: 3,3-dimethyl aspartic acid
synonyms:
- 3,3-dimethyl-L-aspartic acid
- D
- (3S)-3-azanyl-2,2-dimethyl-butanedioic acid
identifiers:
- ns: pdb-ccd
id: DMK
structure: '[O-]C(=O)[C@H](C(C(=O)[O-])(C)C)[NH3+]'
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
DMT:
id: DMT
name: 3-hydroxy-4,4-dimethyl-2-(methylamino)-6-octenoic acid
synonyms:
- 4-[(2E)-but-2-en-1-yl]-2,4,5-trideoxy-4-methyl-2-(methylamino)-D-arabinonic
acid
- X
- (E,2S,3R)-3-hydroxy-4,4-dimethyl-2-methylamino-oct-6-enoic acid
identifiers:
- ns: pdb-ccd
id: DMT
structure: C/C=C/CC([C@H]([C@@H](C(=O)[O-])[NH2+]C)O)(C)C
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
DNL:
id: DNL
name: 6-amino-hexanal
synonyms:
- 6-aminohexanal
- K
identifiers:
- ns: pdb-ccd
id: DNL
structure: '[NH3+]CCCCCC(=O)[O-]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
DNP:
id: DNP
name: 3-amino-alanine
synonyms:
- A
- 3-ammonio-L-alanine
- '[(2S)-2-amino-3-hydroxy-3-oxo-propyl]azanium'
identifiers:
- ns: pdb-ccd
id: DNP
structure: '[O-]C(=O)[C@H](C[NH3+])N'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
DNS:
id: DNS
name: n~6~-{[5-(dimethylamino)-1-naphthyl]sulfonyl}-l-lysine
synonyms:
- (2S)-2-amino-6-[(5-dimethylaminonaphthalen-1-yl)sulfonylamino]hexanoic acid
- K
- N~6~-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-lysine
identifiers:
- ns: pdb-ccd
id: DNS
structure: '[O-]C(=O)[C@H](CCCCNS(=O)(=O)c1cccc2c1cccc2N(C)C)[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 27
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 27
- molecule: Monomer
element: H
position: 27
charge: 1
DNW:
id: DNW
name: 3-[(2,4-dinitrophenyl)amino]-l-alanine
synonyms:
- 3-[(2,4-dinitrophenyl)amino]-L-alanine
- (2S)-2-azanyl-3-[(2,4-dinitrophenyl)amino]propanoic acid
identifiers:
- ns: pdb-ccd
id: DNW
structure: '[O-]C(=O)[C@H](CNc1ccc(cc1[N+](=O)[O-])[N+](=O)[O-])[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
DO2:
id: DO2
name: 5,5-dihydroxy-6-oxo-l-norleucine
synonyms:
- 5,5-dihydroxy-6-oxo-L-norleucine
- (2S)-2-azanyl-5,5-dihydroxy-6-oxo-hexanoic acid
identifiers:
- ns: pdb-ccd
id: DO2
structure: O=CC(CC[C@@H](C(=O)[O-])[NH3+])(O)O
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
DOA:
id: DOA
name: 12-amino-dodecanoic acid
synonyms:
- 12-aminododecanoic acid
- X
identifiers:
- ns: pdb-ccd
id: DOA
structure: '[NH3+]CCCCCCCCCCCC(=O)[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
DON:
id: DON
name: 6-diazenyl-5-oxo-l-norleucine
synonyms:
- (2S)-2-amino-6-diazenyl-5-oxo-hexanoic acid
- L
- 6-diazenyl-5-oxo-L-norleucine
identifiers:
- ns: pdb-ccd
id: DON
structure: '[O-]C(=O)[C@@H]([NH3+])CCC(=O)CN=N'
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
DPL:
id: DPL
name: 4-oxoproline
synonyms:
- P
- (2S)-4-oxopyrrolidine-2-carboxylic acid
- 4-oxo-L-proline
identifiers:
- ns: pdb-ccd
id: DPL
structure: O=C1C[NH2+][C@@H](C1)C(=O)[O-]
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
- molecule: Monomer
element: H
position: 4
charge: 1
DPP:
id: DPP
name: diaminopropanoic acid
synonyms:
- A
- (2S)-2,3-bis(azanyl)propanoic acid
- 3-amino-L-alanine
identifiers:
- ns: pdb-ccd
id: DPP
structure: '[O-]C(=O)[C@H](C[NH3+])N'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
DPQ:
id: DPQ
name: (s)-2-amino-3-(4-hydroxy-3-oxocyclohexa-1,4-dienyl)propanoic acid
synonyms:
- 3-(4-hydroxy-3-oxocyclohexa-1,4-dien-1-yl)-L-alanine
- (2S)-2-amino-3-(4-hydroxy-3-oxo-1-cyclohexa-1,4-dienyl)propanoic acid
- Y
identifiers:
- ns: pdb-ccd
id: DPQ
structure: '[O-]C(=O)[C@@H]([NH3+])CC1=CC(=O)C(=C[CH-]1)O'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
DV7:
id: DV7
name: l-(7-hydroxycoumarin-4-yl)ethylglycine
synonyms:
- (2~{S})-2-azanyl-4-(7-oxidanyl-2-oxidanylidene-chromen-4-yl)butanoic acid
- (2S)-2-amino-4-(7-hydroxy-2-oxo-2H-1-benzopyran-4-yl)butanoic acid
identifiers:
- ns: pdb-ccd
id: DV7
structure: '[O-]C(=O)[C@H](CCc1cc(=O)oc2c1ccc(c2)O)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
DYA:
id: DYA
name: didehydroaspartate
synonyms:
- D
- (Z)-2-azanylbut-2-enedioic acid
identifiers:
- ns: pdb-ccd
id: DYA
structure: '[O-]C(=O)/C=C(/C(=O)[O-])\[NH3+]'
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
DYG:
id: DYG
name: (3s)-3-amino-3-[(4z)-1-(carboxymethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-imidazol-2-yl]propanoic
acid
synonyms:
- DYG
- (3S)-3-amino-3-[(4Z)-1-(carboxymethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-imidazol-2-yl]propanoic
acid
- (3S)-3-amino-3-{(4Z)-1-(carboxymethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-2-yl}propanoic
acid
identifiers:
- ns: pdb-ccd
id: DYG
structure: '[NH3+][C@H](C1=N/C(=C\c2ccc(cc2)O)/C(=O)N1CC(=O)[O-])CC(=O)[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 22
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
DYJ:
id: DYJ
name: 1-[(2e)-4-carboxy-4-oxobut-2-en-2-yl]-l-proline
synonyms:
- P
- (2S)-1-[(E)-5-oxidanyl-4,5-bis(oxidanylidene)pent-2-en-2-yl]pyrrolidine-2-carboxylic
acid
- 1-[(2E)-4-carboxy-4-oxobut-2-en-2-yl]-L-proline
identifiers:
- ns: pdb-ccd
id: DYJ
structure: C/C(=C\C(=O)C(=O)[O-])/N1CCC[C@H]1C(=O)[O-]
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
DYS:
id: DYS
name: s-[5-(2-aminoethyl)-2,3-dihydroxyphenyl]-l-cysteine
synonyms:
- S-[5-(2-aminoethyl)-2,3-dihydroxyphenyl]-L-cysteine
- C
- (2R)-2-amino-3-[5-(2-aminoethyl)-2,3-dihydroxy-phenyl]sulfanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: DYS
structure: '[NH3+]CCc1cc(SC[C@@H](C(=O)[O-])[NH3+])c(c(c1)O)O'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
E0Y:
id: E0Y
name: (3s,5r)-5-[(2r,3r)-1,3-dihydroxybutan-2-yl]-3-({(3r)-1-[(1e)-ethanimidoyl]pyrrolidin-3-yl}sulfanyl)-l-proline
synonyms:
- (3S,5R)-5-[(2R,3R)-1,3-dihydroxybutan-2-yl]-3-({(3R)-1-[(1E)-ethanimidoyl]pyrrolidin-3-yl}sulfanyl)-L-proline
- (5~{R})-5-[(2~{R},3~{R})-1,3-bis(oxidanyl)butan-2-yl]-3-[(3~{R})-1-ethanimidoylpyrrolidin-3-yl]sulfanyl-pyrrolidine-2-carboxylic
acid
identifiers:
- ns: pdb-ccd
id: E0Y
structure: OC[C@@H]([C@H]1CC(C([NH2+]1)C(=O)[O-])S[C@@H]1CCN(C1)C(=[NH2+])C)[C@H](O)C
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
E95:
id: E95
name: 7-methyl-l-tryptophan
synonyms:
- (2~{S})-2-azanyl-3-(7-methyl-1~{H}-indol-3-yl)propanoic acid
identifiers:
- ns: pdb-ccd
id: E95
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1c[nH]c2c1cccc2C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
E9M:
id: E9M
name: n-methyl-l-tryptophan
synonyms:
- (2S)-3-(1H-indol-3-yl)-2-(methylamino)propanoic acid
- N-methyl-L-tryptophan
- W
identifiers:
- ns: pdb-ccd
id: E9M
structure: C[NH2+][C@H](C(=O)[O-])Cc1c[nH]c2c1cccc2
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
E9V:
id: E9V
name: n-methyl-l-histidine
synonyms:
- (2~{S})-3-(1~{H}-imidazol-5-yl)-2-(methylamino)propanoic acid
- N-methyl-L-histidine
identifiers:
- ns: pdb-ccd
id: E9V
structure: '[O-]C(=O)[C@@H]([NH2+]C)Cc1cnc[nH]1'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
ECC:
id: ECC
name: (4s)-4-amino-5-hydroxypentanamide
synonyms:
- (4S)-4-azanyl-5-oxidanyl-pentanamide
- Q
- (4S)-4-amino-5-hydroxypentanamide
identifiers:
- ns: pdb-ccd
id: ECC
structure: NC(=O)CC[C@H]([NH3+])CO
base_monomers:
- Q
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
ECX:
id: ECX
name: s-ethyl-l-cysteine
synonyms:
- (2R)-2-azanyl-3-ethylsulfanyl-propanoic acid
- S-ethyl-L-cysteine
identifiers:
- ns: pdb-ccd
id: ECX
structure: '[O-]C(=O)[C@@H]([NH3+])CSCC'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
EFC:
id: EFC
name: s,s-(2-fluoroethyl)thiocysteine
synonyms:
- (2R)-2-amino-3-(2-fluoroethyldisulfanyl)propanoic acid
- 3-[(2-fluoroethyl)disulfanyl]-L-alanine
- C
identifiers:
- ns: pdb-ccd
id: EFC
structure: '[O-]C(=O)[C@@H]([NH3+])CSSCCF'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
EJA:
id: EJA
name: s-[(1z)-2-carboxy-n-hydroxyethanimidoyl]-l-cysteine
synonyms:
- (2~{R})-2-azanyl-3-[(~{Z})-~{C}-(2-hydroxy-2-oxoethyl)-~{N}-oxidanyl-carbonimidoyl]sulfanyl-propanoic
acid
- S-[(1Z)-2-carboxy-N-hydroxyethanimidoyl]-L-cysteine
identifiers:
- ns: pdb-ccd
id: EJA
structure: O/N=C(/CC(=O)[O-])\SC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
ELY:
id: ELY
name: n~6~,n~6~-diethyl-l-lysine
synonyms:
- (2S)-2-azanyl-6-(diethylamino)hexanoic acid
- N~6~,N~6~-diethyl-L-lysine
identifiers:
- ns: pdb-ccd
id: ELY
structure: CC[NH+](CCCC[C@@H](C(=O)[O-])[NH3+])CC
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
EME:
id: EME
name: n-methyl-l-glutamic acid
synonyms:
- (2S)-2-(methylamino)pentanedioic acid
- N-methyl-L-glutamic acid
identifiers:
- ns: pdb-ccd
id: EME
structure: C[NH2+][C@H](C(=O)[O-])CCC(=O)[O-]
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
EO2:
id: EO2
name: 4,5-dehydro-l-leucine
synonyms:
- (2~{S})-2-azanyl-4-methyl-pent-4-enoic acid
identifiers:
- ns: pdb-ccd
id: EO2
structure: CC(=C)C[C@@H](C(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
ESB:
id: ESB
name: 3-[(3e)-3-(ethylimino)-4-hydroxy-6-oxocyclohexa-1,4-dien-1-yl]-l-alanine
synonyms:
- (2S)-2-amino-3-[(3E)-3-ethylimino-4-hydroxy-6-oxo-1-cyclohexa-1,4-dienyl]propanoic
acid
- Y
- 3-[(3E)-3-(ethylimino)-4-hydroxy-6-oxocyclohexa-1,4-dien-1-yl]-L-alanine
identifiers:
- ns: pdb-ccd
id: ESB
structure: CC/[NH+]=C/1\C=C(C[C@@H](C(=O)[O-])[NH3+])C(=O)C=C1[O-]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
ESC:
id: ESC
name: 2-amino-4-ethyl sulfanyl butyric acid
synonyms:
- S-ethyl-L-homocysteine
- (2S)-2-amino-4-ethylsulfanyl-butanoic acid
- M
identifiers:
- ns: pdb-ccd
id: ESC
structure: CCSCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
ETA:
id: ETA
name: ethanolamine
synonyms:
- 2-aminoethanol
- 2-azanylethanol
identifiers:
- ns: pdb-ccd
id: ETA
structure: OCC[NH3+]
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
- molecule: Monomer
element: H
position: 4
charge: 1
EUP:
id: EUP
name: 4-amino-l-allothreonine
synonyms:
- (2~{S},3~{S})-2,4-bis(azanyl)-3-oxidanyl-butanoic acid
- 4-amino-L-allothreonine
identifiers:
- ns: pdb-ccd
id: EUP
structure: '[NH3+]C[C@@H]([C@@H](C(=O)[O-])[NH3+])O'
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
EXY:
id: EXY
name: 6-[(2r)-oxiran-2-yl]-l-norleucine
synonyms:
- (2S)-2-amino-6-[(2R)-oxiran-2-yl]hexanoic acid
- L
- 6-[(2R)-oxiran-2-yl]-L-norleucine
identifiers:
- ns: pdb-ccd
id: EXY
structure: '[O-]C(=O)[C@H](CCCC[C@@H]1CO1)[NH3+]'
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
EYG:
id: EYG
name: '{(2r,4z)-2-[(1r)-1-amino-3-(methylsulfanyl)propyl]-2-hydroxy-4-[(4-hydroxyphenyl)methylidene]-5-oxoimidazolidin-1-yl}acetic
acid'
synonyms:
- 2-[(2R,4Z)-2-(1-azanyl-3-methylsulfanyl-propyl)-2-hydroxy-4-[(4-hydroxyphenyl)methylidene]-5-oxo-imidazolidin-1-yl]ethanoic
acid
- '[(2R,4Z)-2-[(1R)-1-amino-3-(methylsulfanyl)propyl]-2-hydroxy-4-(4-hydroxybenzylidene)-5-oxoimidazolidin-1-yl]acetic
acid'
identifiers:
- ns: pdb-ccd
id: EYG
structure: CSCCC([C@@]1(O)N/C(=C\c2ccc(cc2)O)/C(=O)N1CC(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 22
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
F2F:
id: F2F
name: 3,4-difluoro-l-phenylalanine
synonyms:
- F
- (2S)-2-amino-3-(3,4-difluorophenyl)propanoic acid
- 3,4-difluoro-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: F2F
structure: '[O-]C(=O)[C@H](Cc1ccc(c(c1)F)F)[NH3+]'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
F2Y:
id: F2Y
name: 3,5-difluoro-l-tyrosine
synonyms:
- 3,5-difluoro-L-tyrosine
- (2S)-2-azanyl-3-[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]propanoic acid
identifiers:
- ns: pdb-ccd
id: F2Y
structure: '[NH3+][C@H](C(=O)[O-])Cc1cc(F)c(c(c1)F)O'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
F3M:
id: F3M
name: methyl 4-amino-2,4,5-trideoxy-5,5,5-trifluoro-l-threo-pentonate
synonyms:
- methyl (3S,4R)-4-azanyl-5,5,5-trifluoro-3-hydroxy-pentanoate
- methyl 4-amino-2,4,5-trideoxy-5,5,5-trifluoro-L-threo-pentonate
identifiers:
- ns: pdb-ccd
id: F3M
structure: COC(=O)C[C@@H]([C@H](C(F)(F)F)N)O
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
F3T:
id: F3T
name: 4-amino-2,4,5-trideoxy-5,5,5-trifluoro-l-threo-pentonic acid
synonyms:
- (3S,4R)-4-azanyl-5,5,5-trifluoro-3-hydroxy-pentanoic acid
- 4-amino-2,4,5-trideoxy-5,5,5-trifluoro-L-threo-pentonic acid
identifiers:
- ns: pdb-ccd
id: F3T
structure: O[C@H]([C@H](C(F)(F)F)N)CC(=O)[O-]
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
F7W:
id: F7W
name: 7-fluorotryptophan
synonyms:
- (2~{S})-2-azanyl-3-(7-fluoranyl-1~{H}-indol-3-yl)propanoic acid
- W
identifiers:
- ns: pdb-ccd
id: F7W
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1c[nH]c2c1cccc2F'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
FAK:
id: FAK
name: n~6~-(trifluoroacetyl)-l-lysine
synonyms:
- K
- (2S)-2-azanyl-6-[2,2,2-tris(fluoranyl)ethanoylamino]hexanoic acid
- N~6~-(trifluoroacetyl)-L-lysine
identifiers:
- ns: pdb-ccd
id: FAK
structure: '[O-]C(=O)[C@H](CCCCNC(=O)C(F)(F)F)[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
FB5:
id: FB5
name: 2-(difluoromethyl)-6-(dihydroxyboranyl)-l-norleucine
synonyms:
- A
- 2-(difluoromethyl)-6-(dihydroxyboranyl)-L-norleucine
- (2S)-2-azanyl-2-[bis(fluoranyl)methyl]-6-(dihydroxyboranyl)hexanoic acid
identifiers:
- ns: pdb-ccd
id: FB5
structure: OB(CCCC[C@](C(=O)[O-])(C(F)F)[NH3+])O
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
FB6:
id: FB6
name: 6-(dihydroxyboranyl)-2-methyl-l-norleucine
synonyms:
- A
- 2-azanyl-6-(dihydroxyboranyl)-2-methyl-hexanoic acid
- 6-(dihydroxyboranyl)-2-methyl-L-norleucine
identifiers:
- ns: pdb-ccd
id: FB6
structure: OB(CCCCC(C(=O)[O-])([NH3+])C)O
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
FC0:
id: FC0
name: n-carboxy-l-phenylalanine
synonyms:
- F
- N-carboxy-L-phenylalanine
- (2S)-2-(carboxyamino)-3-phenyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: FC0
structure: '[O-]C(=O)[C@H](Cc1ccccc1)NC(=O)[O-]'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
FCL:
id: FCL
name: 3-chloro-l-phenylalanine
synonyms:
- F
- 3-chloro-L-phenylalanine
- (2S)-2-amino-3-(3-chlorophenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: FCL
structure: '[O-]C(=O)[C@H](Cc1cccc(c1)Cl)[NH3+]'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
FDL:
id: FDL
name: n~6~-acetyl-n-(4-methyl-2-oxo-2h-chromen-7-yl)-l-lysinamide
synonyms:
- N~6~-acetyl-N-(4-methyl-2-oxo-2H-chromen-7-yl)-L-lysinamide
- (2S)-6-acetamido-2-azanyl-N-(4-methyl-2-oxidanylidene-chromen-7-yl)hexanamide
identifiers:
- ns: pdb-ccd
id: FDL
structure: CC(=O)NCCCC[C@@H](C(=O)Nc1ccc2c(c1)oc(=O)cc2C)[NH3+]
base_monomers:
- K
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
FFM:
id: FFM
name: s-[(1r,2r)-2-hydroxy-1-methyl-2-phosphonoethyl]-l-cysteine
synonyms:
- (2R)-2-azanyl-3-[(1R,2R)-1-hydroxy-1-phosphono-propan-2-yl]sulfanyl-propanoic
acid
identifiers:
- ns: pdb-ccd
id: FFM
structure: '[O-]C(=O)[C@H](CS[C@@H]([C@@H](P(=O)(O)[O-])O)C)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
FGP:
id: FGP
name: 2-amino-3-hydroxy-3-phosphonooxy-propionic acid
synonyms:
- S
- (2S,3S)-2-azanyl-3-oxidanyl-3-phosphonooxy-propanoic acid
- (3S)-3-(phosphonooxy)-L-serine
identifiers:
- ns: pdb-ccd
id: FGP
structure: '[O-]C(=O)[C@H]([C@H](OP(=O)([O-])[O-])O)[NH3+]'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
FHL:
id: FHL
name: (e)-n~6~-[3-carboxy-1-(hydroxymethyl)propylidene]-l-lysine
synonyms:
- (2S)-2-amino-6-[(1,5-dihydroxy-5-oxo-pentan-2-ylidene)amino]hexanoic acid
- K
- (E)-N~6~-[3-carboxy-1-(hydroxymethyl)propylidene]-L-lysine
identifiers:
- ns: pdb-ccd
id: FHL
structure: OC/C(=N/CCCC[C@@H](C(=O)[O-])[NH3+])/CCC(=O)[O-]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
FIO:
id: FIO
name: n~5~-[(1e)-2-fluoroethanimidoyl]-l-ornithine
synonyms:
- N~5~-[(1E)-2-fluoroethanimidoyl]-L-ornithine
- (2S)-2-azanyl-5-(2-fluoranylethanimidoylamino)pentanoic acid
identifiers:
- ns: pdb-ccd
id: FIO
structure: FCC(=[NH2+])NCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
FLA:
id: FLA
name: trifluoroalanine
synonyms:
- A
- (2S)-2-amino-3,3,3-trifluoro-propanoic acid
- 3,3,3-trifluoro-D-alanine
identifiers:
- ns: pdb-ccd
id: FLA
structure: N[C@H](C(F)(F)F)C(=O)[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
FLE:
id: FLE
name: furoyl-leucine
synonyms:
- N-(furan-2-ylcarbonyl)-L-leucine
- (2S)-2-(furan-2-ylcarbonylamino)-4-methyl-pentanoic acid
- L
identifiers:
- ns: pdb-ccd
id: FLE
structure: CC(C[C@@H](C(=O)[O-])NC(=O)c1ccco1)C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
FLT:
id: FLT
name: fluoromalonyl tyrosine
synonyms:
- 2-[4-[(2S)-2-amino-3-hydroxy-3-oxo-propyl]phenoxy]-2-fluoro-propanedioic acid
- '{4-[(2S)-2-amino-2-carboxyethyl]phenoxy}(fluoro)propanedioic acid'
- Y
identifiers:
- ns: pdb-ccd
id: FLT
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)OC(C(=O)[O-])(C(=O)[O-])F'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
FOE:
id: FOE
name: 2-(2-amino-3-oxo-propylsulfanyl)-n-(4-fluoro-phenyl)-n-isopropyl-acetamide
synonyms:
- S-{2-[(4-fluorophenyl)(1-methylethyl)amino]-2-oxoethyl}-L-cysteine
- (2R)-2-amino-3-[2-[(4-fluorophenyl)-propan-2-yl-amino]-2-oxo-ethyl]sulfanyl-propanoic
acid
- C
identifiers:
- ns: pdb-ccd
id: FOE
structure: CC(N(c1ccc(cc1)F)C(=O)CSC[C@@H](C(=O)[O-])[NH3+])C
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
FP9:
id: FP9
name: (4r)-4-fluoro-l-proline
synonyms:
- P
- (2S,4R)-4-fluoranylpyrrolidine-2-carboxylic acid
- (4R)-4-fluoro-L-proline
identifiers:
- ns: pdb-ccd
id: FP9
structure: '[O-]C(=O)[C@@H]1C[C@H](C[NH2+]1)F'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
FPK:
id: FPK
name: 1-formyl-l-proline
synonyms:
- P
- (2S)-1-methanoylpyrrolidine-2-carboxylic acid
- 1-formyl-L-proline
identifiers:
- ns: pdb-ccd
id: FPK
structure: O=CN1CCC[C@H]1C(=O)[O-]
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
FPR:
id: FPR
name: (3s)-3-amino-4-oxo-7-phenylheptanoic acid
synonyms:
- (3S)-3-amino-4-oxo-7-phenylheptanoic acid
- (3S)-3-azanyl-4-oxo-7-phenyl-heptanoic acid
identifiers:
- ns: pdb-ccd
id: FPR
structure: '[O-]C(=O)C[C@@H](C(=O)CCCc1ccccc1)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
FRD:
id: FRD
name: 1-phenyl-2-aminopropane
synonyms:
- (2R)-1-phenylpropan-2-amine
- X
identifiers:
- ns: pdb-ccd
id: FRD
structure: C[C@H](Cc1ccccc1)[NH3+]
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
FT6:
id: FT6
name: 6-fluoro-l-tryptophan
synonyms:
- (2S)-2-amino-3-(6-fluoro-1H-indol-3-yl)propanoic acid
- 6-fluoro-L-tryptophan
- W
identifiers:
- ns: pdb-ccd
id: FT6
structure: '[O-]C(=O)[C@H](Cc1c[nH]c2c1ccc(c2)F)[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
FTR:
id: FTR
name: fluorotryptophane
synonyms:
- 5-fluoro-L-tryptophan
- (2S)-2-amino-3-(5-fluoro-1H-indol-3-yl)propanoic acid
- W
identifiers:
- ns: pdb-ccd
id: FTR
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1c[nH]c2c1cc(F)cc2'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
FTY:
id: FTY
name: deoxy-difluoromethelene-phosphotyrosine
synonyms:
- (2S)-2-amino-3-[4-(difluoro-phosphono-methyl)phenyl]propanoic acid
- Y
- 4-[difluoro(phosphono)methyl]-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: FTY
structure: '[O-]C(=O)[C@H](Cc1ccc(cc1)C(P(=O)([O-])[O-])(F)F)[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
FVA:
id: FVA
name: n-formyl-l-valine
synonyms:
- V
- N-formyl-L-valine
- (2S)-2-formamido-3-methyl-butanoic acid
identifiers:
- ns: pdb-ccd
id: FVA
structure: O=CN[C@H](C(=O)[O-])C(C)C
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 3
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 3
FY2:
id: FY2
name: 2,3-difluoro-l-tyrosine
synonyms:
- (2S)-2-azanyl-3-[2,3-bis(fluoranyl)-4-oxidanyl-phenyl]propanoic acid
- 2,3-difluoro-L-tyrosine
identifiers:
- ns: pdb-ccd
id: FY2
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1ccc(c(c1F)F)O'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
FY3:
id: FY3
name: 2,3,5-trifluoro-l-tyrosine
synonyms:
- (2S)-2-azanyl-3-[2,3,5-tris(fluoranyl)-4-oxidanyl-phenyl]propanoic acid
- 2,3,5-trifluoro-L-tyrosine
identifiers:
- ns: pdb-ccd
id: FY3
structure: '[NH3+][C@H](C(=O)[O-])Cc1cc(F)c(c(c1F)F)[O-]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
FZN:
id: FZN
name: (2s)-2-amino-6-{[(1z)-1-{[(2r,3r,4s,5r)-5-({[(r)-{[(r)-{[(2r,3s,4r,5r)-5-(6-amino-9h-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl]sulfanyl}ethylidene]amino}hexanoic
acid
synonyms:
- (2S)-2-amino-6-[1-[(2R,3R,4S,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxymethyl]-3,4-dihydroxy-oxolan-2-yl]sulfanylethylideneamino]hexanoic
acid
- K
- (2S)-2-amino-6-{[(1Z)-1-{[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl]sulfanyl}ethylidene]amino}hexanoic
acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: FZN
structure: '[O-]C(=O)[C@H](CCCC/N=C(\S[C@H]1O[C@@H]([C@H]([C@H]1O)O)CO[P@](=O)(O[P@@](=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)[O-])[O-])/C)[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 57
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 57
- molecule: Monomer
element: H
position: 57
charge: 1
G3M:
id: G3M
name: (3s)-n~6~-carbamimidoyl-3-hydroxy-l-lysine
synonyms:
- (2~{S},3~{S})-2-azanyl-6-carbamimidamido-3-oxidanyl-hexanoic acid
- (3S)-N~6~-carbamimidoyl-3-hydroxy-L-lysine
identifiers:
- ns: pdb-ccd
id: G3M
structure: O[C@H]([C@@H](C(=O)[O-])[NH3+])CCCNC(=[NH2+])N
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
G8M:
id: G8M
name: (1s,2r)-2-[(s)-amino(carboxy)methyl]cyclobutanecarboxylic acid
synonyms:
- (1S,2R)-2-[(1S)-1-azanyl-2-oxidanyl-2-oxidanylidene-ethyl]cyclobutane-1-carboxylic
acid
- (1S,2R)-2-[(S)-amino(carboxy)methyl]cyclobutanecarboxylic acid
identifiers:
- ns: pdb-ccd
id: G8M
structure: '[NH3+][C@@H]([C@@H]1CC[C@@H]1C(=O)[O-])C(=O)[O-]'
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
GAU:
id: GAU
name: (4s)-4-amino-5-hydroxypentanoic acid
synonyms:
- (4S)-4-amino-5-hydroxypentanoic acid
- E
- (4S)-4-amino-5-hydroxy-pentanoic acid
identifiers:
- ns: pdb-ccd
id: GAU
structure: '[O-]C(=O)CC[C@H]([NH3+])CO'
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
GEE:
id: GEE
name: ethyl glycinate
synonyms:
- ethyl 2-azanylethanoate
- ethyl glycinate
identifiers:
- ns: pdb-ccd
id: GEE
structure: CCOC(=O)CN
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
GFT:
id: GFT
name: (2s)-2-azanyl-3-[cyclohexyloxy(methyl)phosphoryl]oxy-propanoic acid
synonyms:
- S
- O-[(S)-(cyclohexyloxy)(methyl)phosphoryl]-L-serine
- (2S)-2-azanyl-3-[cyclohexyloxy(methyl)phosphoryl]oxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: GFT
structure: '[O-]C(=O)[C@H](CO[P@](=O)(OC1CCCCC1)C)[NH3+]'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
GHC:
id: GHC
name: n-({4-[(2-amino-6-ethyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-5-yl)sulfanyl]phenyl}carbonyl)-l-glutamic
acid
synonyms:
- N-({4-[(2-amino-6-ethyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-5-yl)sulfanyl]phenyl}carbonyl)-L-glutamic
acid
- (2S)-2-[[4-[(2-amino-6-ethyl-4-oxo-3H-thieno[5,4-d]pyrimidin-5-yl)sulfanyl]phenyl]carbonylamino]pentanedioic
acid
identifiers:
- ns: pdb-ccd
id: GHC
structure: CCc1sc2c(c1Sc1ccc(cc1)C(=O)N[C@H](C(=O)[O-])CCC(=O)[O-])c(=O)[nH]c(n2)N
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
GHG:
id: GHG
name: (2s,4s)-2,5-diamino-4-hydroxy-5-oxopentanoic acid (non-preferred name)
synonyms:
- (2S,4S)-2,5-bis(azanyl)-4-hydroxy-5-oxo-pentanoic acid
- Q
- (2S,4S)-2,5-diamino-4-hydroxy-5-oxopentanoic acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: GHG
structure: '[NH3+][C@H](C(=O)[O-])C[C@@H](C(=O)N)O'
base_monomers:
- Q
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
GHW:
id: GHW
name: n-({4-[(2-amino-6-methyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-5-yl)sulfanyl]phenyl}carbonyl)-l-glutamic
acid
synonyms:
- (2S)-2-[[4-[(2-amino-6-methyl-4-oxo-3H-thieno[5,4-d]pyrimidin-5-yl)sulfanyl]phenyl]carbonylamino]pentanedioic
acid
- N-({4-[(2-amino-6-methyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-5-yl)sulfanyl]phenyl}carbonyl)-L-glutamic
acid
identifiers:
- ns: pdb-ccd
id: GHW
structure: '[O-]C(=O)CC[C@@H](C(=O)[O-])NC(=O)c1ccc(cc1)Sc1c(C)sc2c1c(=O)[nH]c(n2)N'
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
GLJ:
id: GLJ
name: 5,5-dihydroxy-l-norvaline
synonyms:
- E
- 5,5-dihydroxy-L-norvaline
- (2S)-2-azanyl-5,5-dihydroxy-pentanoic acid
identifiers:
- ns: pdb-ccd
id: GLJ
structure: '[NH3+][C@H](C(=O)[O-])CCC(O)O'
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
GLZ:
id: GLZ
name: amino-acetaldehyde
synonyms:
- G
- 2-aminoethanal
- aminoacetaldehyde
identifiers:
- ns: pdb-ccd
id: GLZ
structure: '[O-]C(=O)C[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
GME:
id: GME
name: 5-o-methyl-glutamic acid
synonyms:
- (2S)-2-azanyl-5-methoxy-5-oxo-pentanoic acid
- (2S)-2-amino-5-methoxy-5-oxopentanoic acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: GME
structure: COC(=O)CC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
GMO:
id: GMO
name: '{(4z)-2-[(1r,2r)-1-amino-2-hydroxypropyl]-4-[(4-nitrophenyl)methylidene]-5-oxo-4,5-dihydro-1h-imidazol-1-yl}acetic
acid'
synonyms:
- '{(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(4-nitrophenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid'
- 2-[(4~{Z})-2-[(1~{R},2~{R})-1-azanyl-2-oxidanyl-propyl]-4-[(4-nitrophenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
identifiers:
- ns: pdb-ccd
id: GMO
structure: '[O-]C(=O)CN1C(=O)/C(=C/c2ccc(cc2)[N+](=O)[O-])/N=C1[C@H]([C@H](O)C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
GNC:
id: GNC
name: n~2~-methyl-l-glutamine
synonyms:
- N~2~-methyl-L-glutamine
- (2S)-5-azanyl-2-(methylamino)-5-oxidanylidene-pentanoic acid
identifiers:
- ns: pdb-ccd
id: GNC
structure: C[NH2+][C@H](C(=O)[O-])CCC(=O)N
base_monomers:
- Q
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
GSC:
id: GSC
name: 2-ethylthio glycine
synonyms:
- G
- (2S)-amino(ethylsulfanyl)ethanoic acid
- (2S)-2-amino-2-ethylsulfanyl-ethanoic acid
identifiers:
- ns: pdb-ccd
id: GSC
structure: '[O-]C(=O)[C@@H]([NH3+])SCC'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
GSU:
id: GSU
name: o5'-(l-glutamyl-sulfamoyl)-adenosine
synonyms:
- E
- 5'-O-(L-alpha-glutamylsulfamoyl)adenosine
- (4S)-4-amino-5-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxysulfonylamino]-5-oxo-pentanoic
acid
identifiers:
- ns: pdb-ccd
id: GSU
structure: '[O-]C(=O)CC[C@@H](C(=O)[N-]S(=O)(=O)OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)N'
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 29
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
GT9:
id: GT9
name: s-nonyl-cysteine
synonyms:
- S-nonyl-L-cysteine
- (2R)-2-amino-3-nonylsulfanyl-propanoic acid
- C
identifiers:
- ns: pdb-ccd
id: GT9
structure: CCCCCCCCCSC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
GVL:
id: GVL
name: o-[(r)-{[(3r)-4-amino-3-hydroxy-2,2-dimethyl-4-oxobutyl]oxy}(hydroxy)phosphoryl]-l-serine
synonyms:
- O-[(R)-{[(3R)-4-amino-3-hydroxy-2,2-dimethyl-4-oxobutyl]oxy}(hydroxy)phosphoryl]-L-serine
- S
- (2S)-2-amino-3-[[(3R)-4-amino-3-hydroxy-2,2-dimethyl-4-oxo-butoxy]-hydroxy-phosphoryl]oxy-propanoic
acid
identifiers:
- ns: pdb-ccd
id: GVL
structure: '[NH3+][C@H](C(=O)[O-])COP(=O)(OCC([C@H](C(=O)N)O)(C)C)[O-]'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
GZB:
id: GZB
name: 2-benzamidoethanoic acid
synonyms:
- 2-benzamidoethanoic acid
identifiers:
- ns: pdb-ccd
id: GZB
structure: O=C(c1ccccc1)NCC(=O)[O-]
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
H14:
id: H14
name: (2s,3r)-beta-hydroxy-phenylalanine
synonyms:
- F
- (betaR)-beta-hydroxy-L-phenylalanine
- (2S,3R)-2-amino-3-hydroxy-3-phenyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: H14
structure: O[C@@H]([C@@H](C(=O)[O-])[NH3+])c1ccccc1
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
H5M:
id: H5M
name: trans-3-hydroxy-5-methylproline
synonyms:
- P
- (2S,3S,5S)-3-hydroxy-5-methyl-pyrrolidine-2-carboxylic acid
- (3S,5S)-3-hydroxy-5-methyl-L-proline
identifiers:
- ns: pdb-ccd
id: H5M
structure: O[C@H]1C[C@@H]([NH2+][C@@H]1C(=O)[O-])C
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
H7V:
id: H7V
name: 3-cyclohexyl-n-methyl-l-alanine
synonyms:
- A
- 3-cyclohexyl-N-methyl-L-alanine
- (2~{S})-3-cyclohexyl-2-(methylamino)propanoic acid
identifiers:
- ns: pdb-ccd
id: H7V
structure: '[O-]C(=O)[C@H](CC1CCCCC1)[NH2+]C'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
HAR:
id: HAR
name: n-omega-hydroxy-l-arginine
synonyms:
- N~5~-(N-hydroxycarbamimidoyl)-L-ornithine
- (2S)-2-amino-5-[(N-hydroxycarbamimidoyl)amino]pentanoic acid
- R
identifiers:
- ns: pdb-ccd
id: HAR
structure: ONC(=[NH2+])NCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
HBN:
id: HBN
name: n-(2-naphthyl)histidinamide
synonyms:
- 2-amino-3-(3H-imidazol-4-yl)-N-naphthalen-2-yl-propanamide
- N-naphthalen-2-yl-D-histidinamide
- H
identifiers:
- ns: pdb-ccd
id: HBN
structure: O=C(C(Cc1cnc[nH]1)[NH3+])Nc1ccc2c(c1)cccc2
base_monomers:
- H
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
HCL:
id: HCL
name: (2s)-2-azanyl-2-[2-chloranyl-3,5-bis(oxidanyl)phenyl]ethanoic acid
synonyms:
- (2S)-2-azanyl-2-[2-chloranyl-3,5-bis(oxidanyl)phenyl]ethanoic acid
identifiers:
- ns: pdb-ccd
id: HCL
structure: Oc1cc(O)c(c(c1)[C@@H](C(=O)[O-])[NH3+])Cl
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
HCM:
id: HCM
name: (2s)-2-amino-4-(methyldisulfanyl)butanoic acid
synonyms:
- (2S)-2-azanyl-4-(methyldisulfanyl)butanoic acid
- (2S)-2-amino-4-(methyldisulfanyl)butanoic acid
identifiers:
- ns: pdb-ccd
id: HCM
structure: CSSCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
HCS:
id: HCS
name: 2-amino-4-mercapto-butyric acid
synonyms:
- (2S)-2-amino-4-sulfanyl-butanoic acid
- X
- L-homocysteine
identifiers:
- ns: pdb-ccd
id: HCS
structure: '[O-]C(=O)[C@@H]([NH3+])CCS'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
HG7:
id: HG7
name: (2s)-2-azanyl-n-[3-(dimethylamino)propyl]-2-(3-hydroxyphenyl)ethanamide
synonyms:
- (2S)-2-azanyl-N-[3-(dimethylamino)propyl]-2-(3-hydroxyphenyl)ethanamide
identifiers:
- ns: pdb-ccd
id: HG7
structure: C[NH+](CCCNC(=O)[C@H](c1cccc(c1)O)[NH3+])C
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
HGL:
id: HGL
name: (2s)-2-amino-4-(2-amino-6-oxo-1,6-dihydro-9h-purin-9-yl)butanoic acid
synonyms:
- (2S)-2-amino-4-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)butanoic acid
- X
- (2S)-2-amino-4-(2-amino-6-oxo-1H-purin-9-yl)butanoic acid
identifiers:
- ns: pdb-ccd
id: HGL
structure: '[O-]C(=O)[C@H](CCn1cnc2c1nc(N)[nH]c2=O)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
HHK:
id: HHK
name: (2s)-2,8-diaminooctanoic acid
synonyms:
- AK
- (2S)-2,8-diaminooctanoic acid
identifiers:
- ns: pdb-ccd
id: HHK
structure: '[NH3+]CCCCCC[C@@H](C(=O)[O-])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
HIX:
id: HIX
name: 3-(1h-1,2,3-triazol-5-yl)-l-alanine
synonyms:
- 3-(1H-1,2,3-triazol-5-yl)-L-alanine
- (2S)-2-azanyl-3-(1H-1,2,3-triazol-5-yl)propanoic acid
identifiers:
- ns: pdb-ccd
id: HIX
structure: '[O-]C(=O)[C@H](Cc1cnn[nH]1)[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
HL2:
id: HL2
name: (2s,3r)-2-amino-3-hydroxy-4-methylpentanoic acid
synonyms:
- (2S,3R)-2-amino-3-hydroxy-4-methylpentanoic acid (non-preferred name)
- (2S,3R)-2-azanyl-3-hydroxy-4-methyl-pentanoic acid
- L
identifiers:
- ns: pdb-ccd
id: HL2
structure: CC([C@H]([C@@H](C(=O)[O-])[NH3+])O)C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
HLU:
id: HLU
name: beta-hydroxyleucine
synonyms:
- (2S,3S)-2-amino-3-hydroxy-4-methyl-pentanoic acid
- (2S,3S)-2-amino-3-hydroxy-4-methylpentanoic acid (non-preferred name)
- L
identifiers:
- ns: pdb-ccd
id: HLU
structure: CC([C@@H]([C@@H](C(=O)[O-])[NH3+])O)C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
HLX:
id: HLX
name: 5-methyl-l-norleucine
synonyms:
- (2S)-2-azanyl-5-methyl-hexanoic acid
- 5-methyl-L-norleucine
identifiers:
- ns: pdb-ccd
id: HLX
structure: '[NH3+][C@H](C(=O)[O-])CCC(C)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
HLY:
id: HLY
name: (3~{r})-5-[[(5~{s})-5-azanyl-6-oxidanyl-6-oxidanylidene-hexyl]amino]-3-methyl-3-oxidanyl-5-oxidanylidene-pentanoic
acid
synonyms:
- (3~{R})-5-[[(5~{S})-5-azanyl-6-oxidanyl-6-oxidanylidene-hexyl]amino]-3-methyl-3-oxidanyl-5-oxidanylidene-pentanoic
acid
- K
identifiers:
- ns: pdb-ccd
id: HLY
structure: O=C(C[C@](CC(=O)[O-])(O)C)NCCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
HM8:
id: HM8
name: 2-[(1s,2r)-1-amino-2-(sulfooxy)propyl]-5-hydroxy-1,3-oxazole-4-carbothioic
o-acid
synonyms:
- 2-[(1S,2R)-1-azanyl-2-sulfooxy-propyl]-5-hydroxy-1,3-oxazole-4-carbothioic O-acid
- 2-[(1S,2R)-1-amino-2-(sulfooxy)propyl]-5-hydroxy-1,3-oxazole-4-carbothioic O-acid
identifiers:
- ns: pdb-ccd
id: HM8
structure: C[C@H]([C@@H](c1oc(c(n1)C(=S)O)[O-])N)OS(=O)(=O)[O-]
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
HM9:
id: HM9
name: 6-(3-carbamimidamidopropyl)-3,5-dihydroxypyrazine-2-carbothioic s-acid
synonyms:
- 6-(3-carbamimidamidopropyl)-3,5-dihydroxypyrazine-2-carbothioic S-acid
- 6-(3-carbamimidamidopropyl)-3,5-dihydroxy-pyrazine-2-carbothioic S-acid
identifiers:
- ns: pdb-ccd
id: HM9
structure: Oc1nc(O)c(nc1CCCNC(=[NH2+])N)C(=O)[S-]
l_bond_atoms:
- molecule: Monomer
element: N
position: 3
HMR:
id: HMR
name: beta-homoarginine
synonyms:
- (3S)-3-amino-6-carbamimidamidohexanoic acid
- (3S)-3-amino-6-carbamimidamido-hexanoic acid
- R
identifiers:
- ns: pdb-ccd
id: HMR
structure: '[O-]C(=O)C[C@H](CCCNC(=[NH2+])N)[NH3+]'
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
HNC:
id: HNC
name: s-[(1s,2r)-2-hydroxy-1-(2-oxoethyl)heptyl]-l-cysteine
synonyms:
- S-[(3S,4R)-4-hydroxy-1-oxononan-3-yl]-L-cysteine
- (2R)-2-azanyl-3-[(3S,4R)-4-hydroxy-1-oxo-nonan-3-yl]sulfanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: HNC
structure: CCCCC[C@H]([C@@H](SC[C@@H](C(=O)[O-])[NH3+])CC=O)O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
HOX:
id: HOX
name: 4-amino-l-phenylalanine
synonyms:
- 4-amino-L-phenylalanine
- (2S)-3-(4-aminophenyl)-2-azanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: HOX
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)N'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
HPE:
id: HPE
name: homophenylalanine
synonyms:
- F
- (2S)-2-amino-4-phenylbutanoic acid
- (2S)-2-amino-4-phenyl-butanoic acid
identifiers:
- ns: pdb-ccd
id: HPE
structure: '[NH3+][C@H](C(=O)[O-])CCc1ccccc1'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
HPQ:
id: HPQ
name: homophenylalaninylmethane
synonyms:
- F
- (3S)-3-amino-5-phenyl-pentan-2-one
- (3S)-3-amino-5-phenylpentan-2-one
identifiers:
- ns: pdb-ccd
id: HPQ
structure: '[NH3+][C@H](C(=O)C)CCc1ccccc1'
base_monomers:
- F
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
HQA:
id: HQA
name: 3-(8-hydroxyquinolin-3-yl)-l-alanine
synonyms:
- A
- 3-(8-hydroxyquinolin-3-yl)-L-alanine
- (2S)-2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid
identifiers:
- ns: pdb-ccd
id: HQA
structure: '[O-]C(=O)[C@H](Cc1cnc2c(c1)cccc2O)[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
HR7:
id: HR7
name: (3s)-3-amino-6-[(diaminomethylidene)amino]hexanoic acid
synonyms:
- (3S)-3-amino-6-[(diaminomethylidene)amino]hexanoic acid
- (3S)-3-azanyl-6-[bis(azanyl)methylideneamino]hexanoic acid
- R
identifiers:
- ns: pdb-ccd
id: HR7
structure: '[O-]C(=O)C[C@H](CCC[NH+]=C(N)N)[NH3+]'
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
HRG:
id: HRG
name: l-homoarginine
synonyms:
- N~6~-carbamimidoyl-L-lysine
- (2S)-2-amino-6-carbamimidamido-hexanoic acid
- R
identifiers:
- ns: pdb-ccd
id: HRG
structure: NC(=[NH2+])NCCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
HRP:
id: HRP
name: 5-hydroxy-l-tryptophan
synonyms:
- 5-hydroxy-D-tryptophan
- (2R)-2-amino-3-(5-hydroxy-1H-indol-3-yl)propanoic acid
- W
identifiers:
- ns: pdb-ccd
id: HRP
structure: '[O-]C(=O)[C@H]([NH3+])Cc1c[nH]c2c1cc(O)cc2'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
HS8:
id: HS8
name: 3-(1-sulfo-1h-imidazol-3-ium-4-yl)-l-alanine
synonyms:
- 3-(1-sulfo-1H-imidazol-3-ium-4-yl)-L-alanine
- (2S)-2-amino-3-(1-sulfoimidazol-3-ium-4-yl)propanoic acid
- H
identifiers:
- ns: pdb-ccd
id: HS8
structure: '[O-]C(=O)[C@H](Cc1ncn(c1)S(=O)(=O)[O-])[NH3+]'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
HS9:
id: HS9
name: n-alpha-methyl-l-histidinamide
synonyms:
- (2S)-3-(1H-imidazol-4-yl)-2-methylamino-propanamide
- Nalpha-methyl-L-histidinamide
- H
identifiers:
- ns: pdb-ccd
id: HS9
structure: C[NH2+][C@H](C(=O)N)Cc1c[nH]cn1
base_monomers:
- H
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
HSE:
id: HSE
name: l-homoserine
synonyms:
- S
- (2S)-2-amino-4-hydroxy-butanoic acid
- L-homoserine
identifiers:
- ns: pdb-ccd
id: HSE
structure: '[O-]C(=O)[C@@H]([NH3+])CCO'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
HSK:
id: HSK
name: 3-hydroxy-l-histidine
synonyms:
- (2S)-2-azanyl-3-(3-oxidanylimidazol-4-yl)propanoic acid
- 3-hydroxy-L-histidine
identifiers:
- ns: pdb-ccd
id: HSK
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1cncn1O'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
HSL:
id: HSL
name: homoserine lactone
synonyms:
- S
- (3S)-3-aminodihydrofuran-2(3H)-one
- (3S)-3-aminooxolan-2-one
identifiers:
- ns: pdb-ccd
id: HSL
structure: O=C1OCC[C@@H]1[NH3+]
base_monomers:
- S
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
HSO:
id: HSO
name: l-histidinol
synonyms:
- 4-[(2S)-2-amino-3-hydroxypropyl]-1H-imidazol-3-ium
- H
- (2S)-2-azanyl-3-(1H-imidazol-3-ium-4-yl)propan-1-ol
identifiers:
- ns: pdb-ccd
id: HSO
structure: OC[C@@H]([NH3+])Cc1c[nH]cn1
base_monomers:
- H
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
HSV:
id: HSV
name: l-histidinal
synonyms:
- 4-[(2S)-2-amino-3-oxopropyl]-1H-imidazol-3-ium
- H
- (2S)-2-azanyl-3-(1H-imidazol-3-ium-4-yl)propanal
identifiers:
- ns: pdb-ccd
id: HSV
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1c[nH]cn1'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
HT7:
id: HT7
name: (3s)-3-amino-4-(1h-indol-3-yl)butanoic acid
synonyms:
- (3S)-3-azanyl-4-(1H-indol-3-yl)butanoic acid
- (3S)-3-amino-4-(1H-indol-3-yl)butanoic acid
- W
identifiers:
- ns: pdb-ccd
id: HT7
structure: '[O-]C(=O)C[C@H](Cc1c[nH]c2c1cccc2)[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
HTI:
id: HTI
name: (4s)-4-{[(2s)-2-amino-3-oxopropyl]sulfanyl}-l-homoserine
synonyms:
- (4R)-4-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-L-homoserine
- (2S,4R)-2-amino-4-[(2R)-2-amino-3-hydroxy-3-oxo-propyl]sulfanyl-4-hydroxy-butanoic
acid
- C
identifiers:
- ns: pdb-ccd
id: HTI
structure: O[C@@H](C[C@@H](C(=O)[O-])[NH3+])SC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
HZP:
id: HZP
name: (4s)-4-hydroxy-l-proline
synonyms:
- P
- (2S,4S)-4-hydroxypyrrolidine-2-carboxylic acid
- (4S)-4-hydroxy-L-proline
identifiers:
- ns: pdb-ccd
id: HZP
structure: '[O-]C(=O)[C@@H]1C[C@@H](C[NH2+]1)O'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
I2M:
id: I2M
name: 3-methyl-l-alloisoleucine
synonyms:
- 3-methyl-L-alloisoleucine
- (2S)-2-amino-3,3-dimethyl-pentanoic acid
- I
identifiers:
- ns: pdb-ccd
id: I2M
structure: CCC([C@@H](C(=O)[O-])[NH3+])(C)C
base_monomers:
- I
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
I4G:
id: I4G
name: n-(2-methylpropyl)glycine
synonyms:
- 2-(2-methylpropylamino)ethanoic acid
- N-(2-methylpropyl)glycine
identifiers:
- ns: pdb-ccd
id: I4G
structure: CC(C[NH2+]CC(=O)[O-])C
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
- molecule: Monomer
element: H
position: 4
charge: 1
I58:
id: I58
name: 4r-fluoro-n6-ethanimidoyl-l-lysine
synonyms:
- (2S,4R)-2-amino-6-(ethanimidoylamino)-4-fluoro-hexanoic acid
- K
- (4R)-N~6~-[(1Z)-ethanimidoyl]-4-fluoro-L-lysine
identifiers:
- ns: pdb-ccd
id: I58
structure: F[C@@H](C[C@@H](C(=O)[O-])[NH3+])CCNC(=[NH2+])C
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
IAM:
id: IAM
name: 4-[(isopropylamino)methyl]phenylalanine
synonyms:
- A
- 4-{[(1-methylethyl)amino]methyl}-L-phenylalanine
- (2S)-2-amino-3-[4-[(propan-2-ylamino)methyl]phenyl]propanoic acid
identifiers:
- ns: pdb-ccd
id: IAM
structure: CC([NH2+]Cc1ccc(cc1)C[C@@H](C(=O)[O-])[NH3+])C
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
ICY:
id: ICY
name: s-(2-iodobenzyl)-l-cysteine
synonyms:
- (2R)-2-azanyl-3-[(2-iodophenyl)methylsulfanyl]propanoic acid
- S-(2-iodobenzyl)-L-cysteine
identifiers:
- ns: pdb-ccd
id: ICY
structure: '[O-]C(=O)[C@H](CSCc1ccccc1I)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
IEL:
id: IEL
name: n~6~-[(1z)-ethanimidoyl]-l-lysine
synonyms:
- N~6~-[(1Z)-ethanimidoyl]-L-lysine
- K
- (2S)-2-amino-6-(ethanimidoylamino)hexanoic acid
identifiers:
- ns: pdb-ccd
id: IEL
structure: CC(=[NH2+])NCCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
IEY:
id: IEY
name: 2-((1e)-2-(5-imidazolyl)ethenyl)-4-(p-hydroxybenzylidene)-5-imidazolinone
synonyms:
- 2-[5-hydroxy-4-[(4-hydroxyphenyl)methyl]-2-[(E)-2-(1H-imidazol-4-yl)ethenyl]imidazol-1-yl]ethanoic
acid
- HYG
- '{5-hydroxy-4-(4-hydroxybenzyl)-2-[(E)-2-(1H-imidazol-4-yl)ethenyl]-1H-imidazol-1-yl}acetic
acid'
identifiers:
- ns: pdb-ccd
id: IEY
structure: '[O-]C(=O)Cn1c(/C=C/c2c[nH]cn2)[nH+]c(c1O)Cc1ccc(cc1)O'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
IGL:
id: IGL
name: alpha-amino-2-indanacetic acid
synonyms:
- G
- (2R)-2-amino-2-(2,3-dihydro-1H-inden-2-yl)ethanoic acid
- (2R)-amino(2,3-dihydro-1H-inden-2-yl)ethanoic acid
identifiers:
- ns: pdb-ccd
id: IGL
structure: '[NH3+][C@@H](C(=O)[O-])C1Cc2c(C1)cccc2'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
IIC:
id: IIC
name: 4-imidazolmethylene-5-imidazolone chromophore
synonyms:
- SHG
- 2-[2-[(1R)-1-amino-2-hydroxy-ethyl]-4-(3H-imidazol-4-ylmethyl)-5-oxo-2H-imidazol-1-yl]ethanoic
acid
- '[(2S)-2-[(1R)-1-amino-2-hydroxyethyl]-4-(1H-imidazol-5-ylmethyl)-5-oxo-2,5-dihydro-1H-imidazol-1-yl]acetic
acid'
identifiers:
- ns: pdb-ccd
id: IIC
structure: OC[C@@H](C1N=C(C(=O)N1CC(=O)[O-])Cc1cnc[nH]1)[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
IIL:
id: IIL
name: iso-isoleucine
synonyms:
- (2S,3R)-2-amino-3-methyl-pentanoic acid
- L-alloisoleucine
- I
identifiers:
- ns: pdb-ccd
id: IIL
structure: CC[C@H]([C@@H](C(=O)[O-])[NH3+])C
base_monomers:
- I
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
ILM:
id: ILM
name: methyl l-isoleucinate
synonyms:
- methyl L-isoleucinate
- methyl (2S,3S)-2-azanyl-3-methyl-pentanoate
identifiers:
- ns: pdb-ccd
id: ILM
structure: CC[C@@H]([C@@H](C(=O)OC)[NH3+])C
base_monomers:
- I
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
IOR:
id: IOR
name: n~5~-[(5r)-5-methyl-4-oxo-4,5-dihydro-1h-imidazol-2-yl]-l-ornithine
synonyms:
- N~5~-[(5R)-5-methyl-4-oxo-4,5-dihydro-1H-imidazol-2-yl]-L-ornithine
- (2S)-2-azanyl-5-[[(5R)-5-methyl-4-oxidanylidene-1,5-dihydroimidazol-2-yl]amino]pentanoic
acid
identifiers:
- ns: pdb-ccd
id: IOR
structure: '[O-]C(=O)[C@H](CCCNC1=[NH+]C(=O)[C@H](N1)C)[NH3+]'
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
IPG:
id: IPG
name: n-isopropyl glycine
synonyms:
- G
- N-(1-methylethyl)glycine
- 2-(propan-2-ylamino)ethanoic acid
identifiers:
- ns: pdb-ccd
id: IPG
structure: CC([NH2+]CC(=O)[O-])C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 3
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 3
- molecule: Monomer
element: H
position: 3
charge: 1
IZO:
id: IZO
name: (2s)-2-aminohex-5-ynoic acid
synonyms:
- M
- (2S)-2-aminohex-5-ynoic acid
identifiers:
- ns: pdb-ccd
id: IZO
structure: '[O-]C(=O)[C@@H]([NH3+])CCC#C'
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
J9Y:
id: J9Y
name: (2s)-2-amino-5-{[(e)-amino(methylamino)methylidene](hydroxy)azaniumyl}pentanoate
synonyms:
- (2~{S})-2-azanyl-5-[(~{E})-[azanyl(methylamino)methylidene]-oxidanyl-azaniumyl]pentanoate
- (2S)-2-amino-5-{[(E)-amino(methylamino)methylidene](hydroxy)azaniumyl}pentanoate
identifiers:
- ns: pdb-ccd
id: J9Y
structure: CN/C(=[N+](\CCC[C@@H](C(=O)[O-])[NH3+])/[O-])/[NH3+]
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
JJJ:
id: JJJ
name: s-(pyridin-3-ylcarbonyl)-l-cysteine
synonyms:
- S-(pyridin-3-ylcarbonyl)-L-cysteine
- C
- (2R)-2-azanyl-3-pyridin-3-ylcarbonylsulfanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: JJJ
structure: '[O-]C(=O)[C@H](CSC(=O)c1cccnc1)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
JJK:
id: JJK
name: s-[(s)-hydroxy(pyridin-3-yl)methyl]-l-cysteine
synonyms:
- S-[(S)-hydroxy(pyridin-3-yl)methyl]-L-cysteine
- (2R)-2-azanyl-3-[(S)-hydroxy(pyridin-3-yl)methyl]sulfanyl-propanoic acid
- C
identifiers:
- ns: pdb-ccd
id: JJK
structure: '[O-]C(=O)[C@H](CS[C@@H](c1cccnc1)O)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
JJL:
id: JJL
name: s-[(s)-hydroxy(5-methoxypyridin-3-yl)methyl]-l-cysteine
synonyms:
- (2R)-2-azanyl-3-[(S)-hydroxy-(5-methoxypyridin-3-yl)methyl]sulfanyl-propanoic
acid
- S-[(S)-hydroxy(5-methoxypyridin-3-yl)methyl]-L-cysteine
- C
identifiers:
- ns: pdb-ccd
id: JJL
structure: COc1cncc(c1)[C@H](SC[C@@H](C(=O)[O-])[NH3+])O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
K1R:
id: K1R
name: (2s)-2-amino-4-[({[(2r)-2-amino-2-carboxyethyl]thio}amino)sulfinyl]butanoic
acid
synonyms:
- (2S)-2-amino-4-[(R)-({[(2R)-2-amino-2-carboxyethyl]sulfanyl}amino)sulfinyl]butanoic
acid
- C
- (2S)-2-amino-4-[(2R)-2-amino-3-hydroxy-3-oxo-propyl]sulfanylsulfinamoyl-butanoic
acid
identifiers:
- ns: pdb-ccd
id: K1R
structure: O=[S@](CC[C@@H](C(=O)[O-])[NH3+])NSC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
K5L:
id: K5L
name: (2~{r})-2-azanyl-3-(3-oxidanyl-3-oxidanylidene-propanoyl)oxy-propanoic acid
synonyms:
- S
- (2~{R})-2-azanyl-3-(3-oxidanyl-3-oxidanylidene-propanoyl)oxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: K5L
structure: '[O-]C(=O)CC(=O)OC[C@H](C(=O)[O-])[NH3+]'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
KBE:
id: KBE
name: beta-lysine
synonyms:
- (3S)-3,6-bis(azanyl)hexanoic acid
identifiers:
- ns: pdb-ccd
id: KBE
structure: '[NH3+]CCC[C@@H](CC(=O)[O-])[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
KCR:
id: KCR
name: n-6-crotonyl-l-lysine
synonyms:
- (2S)-2-azanyl-6-[[(E)-but-2-enoyl]amino]hexanoic acid
- N~6~-[(2E)-but-2-enoyl]-L-lysine
identifiers:
- ns: pdb-ccd
id: KCR
structure: C/C=C/C(=O)NCCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
KEO:
id: KEO
name: e(r)-beta-lysyl-hydroxylysine
synonyms:
- (2~{S},4~{S})-2-azanyl-6-[[(3~{S})-3,6-bis(azanyl)hexanoyl]amino]-4-oxidanyl-hexanoic
acid
- K
identifiers:
- ns: pdb-ccd
id: KEO
structure: '[NH3+]CCC[C@@H](CC(=O)NCC[C@@H](C[C@@H](C(=O)[O-])[NH3+])O)[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 21
l_bond_atoms:
- molecule: Monomer
element: N
position: 24
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 24
- molecule: Monomer
element: H
position: 24
charge: 1
KGC:
id: KGC
name: n~6~-[(2r)-2-carboxy-5-oxotetrahydrofuran-2-yl]-l-lysine
synonyms:
- K
- N~6~-[(2R)-2-carboxy-5-oxotetrahydrofuran-2-yl]-L-lysine
- (2R)-2-[[(5S)-5-amino-6-hydroxy-6-oxo-hexyl]amino]-5-oxo-oxolane-2-carboxylic
acid
identifiers:
- ns: pdb-ccd
id: KGC
structure: O=C1CC[C@](O1)(NCCCC[C@@H](C(=O)[O-])[NH3+])C(=O)[O-]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 21
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
KHB:
id: KHB
name: n~6~-[(3s)-3-hydroxybutanoyl]-l-lysine
synonyms:
- N~6~-[(3S)-3-hydroxybutanoyl]-L-lysine
- (2~{S})-2-azanyl-6-[[(3~{S})-3-oxidanylbutanoyl]amino]hexanoic acid
identifiers:
- ns: pdb-ccd
id: KHB
structure: C[C@@H](CC(=O)NCCCC[C@@H](C(=O)[O-])[NH3+])O
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
KNB:
id: KNB
name: 3-(methylsulfonyl)-l-alanine
synonyms:
- A
- (2R)-2-azanyl-3-methylsulfonyl-propanoic acid
- 3-(methylsulfonyl)-L-alanine
identifiers:
- ns: pdb-ccd
id: KNB
structure: '[O-]C(=O)[C@H](CS(=O)(=O)C)[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
KOR:
id: KOR
name: l-homocysteine-s-n-s-l-cysteine
synonyms:
- M
- (2S)-2-amino-4-[[(R)-[(2R)-2-amino-3-hydroxy-3-oxo-propyl]sulfinyl]amino]sulfanyl-butanoic
acid
- S-({(R)-[(2R)-2-amino-2-carboxyethyl]sulfinyl}amino)-L-homocysteine
identifiers:
- ns: pdb-ccd
id: KOR
structure: O=[S@](C[C@@H](C(=O)[O-])[NH3+])[N-]SCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
KPF:
id: KPF
name: n-(1-carboxy-2-fluoro-ethenyl) lysine
synonyms:
- (2S)-2-azanyl-6-[(Z)-(3-fluoranyl-1-oxidanyl-1-oxidanylidene-propan-2-ylidene)amino]hexanoic
acid
- K
identifiers:
- ns: pdb-ccd
id: KPF
structure: FC/C(=N\CCCC[C@@H](C(=O)[O-])[NH3+])/C(=O)[O-]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
KPY:
id: KPY
name: (2r)-2-azanyl-3-[2-[(e)-(1-oxidanyl-1-oxidanylidene-propan-2-ylidene)amino]ethylsulfanyl]propanoic
acid
synonyms:
- (2R)-2-azanyl-3-[2-[(E)-(1-oxidanyl-1-oxidanylidene-propan-2-ylidene)amino]ethylsulfanyl]propanoic
acid
- K
- S-{2-[(E)-(1-carboxyethylidene)amino]ethyl}-L-cysteine
identifiers:
- ns: pdb-ccd
id: KPY
structure: '[NH3+][C@H](C(=O)[O-])CSCC/N=C(/C(=O)[O-])\C'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
KST:
id: KST
name: n~6~-(5-carboxy-3-thienyl)-l-lysine
synonyms:
- K
- 4-[[(5S)-5-amino-6-hydroxy-6-oxo-hexyl]amino]thiophene-2-carboxylic acid
- N~6~-(5-carboxythiophen-3-yl)-L-lysine
identifiers:
- ns: pdb-ccd
id: KST
structure: '[NH3+][C@H](C(=O)[O-])CCCCNc1csc(c1)C(=O)[O-]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
KWS:
id: KWS
name: '{2-[(1r,2r)-1-amino-2-hydroxypropyl]-4-methylidene-5-oxo-4,5-dihydro-1h-imidazol-1-yl}acetic
acid'
synonyms:
- '{2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-methylidene-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid'
- 2-[2-[(1R,2R)-1-azanyl-2-oxidanyl-propyl]-4-methylidene-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
identifiers:
- ns: pdb-ccd
id: KWS
structure: '[O-]C(=O)CN1C(=O)C(=C)N=C1[C@H]([C@H](O)C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
KYN:
id: KYN
name: (2s)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid
synonyms:
- (2S)-4-(2-aminophenyl)-2-azanyl-4-oxidanylidene-butanoic acid
- (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid
- W
identifiers:
- ns: pdb-ccd
id: KYN
structure: '[O-]C(=O)[C@H](CC(=O)c1ccccc1N)[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
KYQ:
id: KYQ
name: (e)-n~6~-(1-carboxy-2-hydroxyethylidene)-l-lysine
synonyms:
- (E)-N~6~-(1-carboxy-2-hydroxyethylidene)-L-lysine
- (2S)-2-amino-6-[(1,3-dihydroxy-1-oxo-propan-2-ylidene)amino]hexanoic acid
- K
identifiers:
- ns: pdb-ccd
id: KYQ
structure: OC/C(=N\CCCC[C@@H](C(=O)[O-])[NH3+])/C(=O)[O-]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
L2A:
id: L2A
name: (2s,5s,8s,11s,15e,20s)-20-amino-2-(carboxymethyl)-11,20-dimethyl-5,8-bis(2-methylpropyl)-3,6,9,21-tetraoxo-1,4,7,10-tetraazacyclohenicos-15-ene-11-carboxylic
acid
synonyms:
- (2S,5S,8S,11S,15E,20S)-20-amino-2-(carboxymethyl)-11,20-dimethyl-5,8-bis(2-methylpropyl)-3,6,9,21-tetraoxo-1,4,7,10-tetraazacyclohenicos-15-ene-11-carboxylic
acid
- (2S,5S,8S,11S,15E,20S)-20-amino-2-(carboxymethyl)-11,20-dimethyl-5,8-bis(2-methylpropyl)-3,6,9,21-tetraoxo-1,4,7,10-tetrazacyclohenicos-15-ene-11-carboxylic
acid
- X
identifiers:
- ns: pdb-ccd
id: L2A
structure: CC(C[C@@H]1NC(=O)[C@H](CC(=O)[O-])NC(=O)[C@@](C)([NH3+])CCC/C=C/CCC[C@@](NC(=O)[C@@H](NC1=O)CC(C)C)(C)C(=O)[O-])C
r_bond_atoms:
- molecule: Monomer
element: C
position: 46
l_bond_atoms:
- molecule: Monomer
element: N
position: 33
r_displaced_atoms:
- molecule: Monomer
element: O
position: 48
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 33
L3O:
id: L3O
name: (2s,3s)-3-amino-2-hydroxy-5-methylhexanoic acid
synonyms:
- (2S,3S)-3-amino-2-hydroxy-5-methyl-hexanoic acid
- L
- (2S,3S)-3-amino-2-hydroxy-5-methylhexanoic acid
identifiers:
- ns: pdb-ccd
id: L3O
structure: '[NH3+][C@H]([C@@H](C(=O)[O-])O)CC(C)C'
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
L5P:
id: L5P
name: (2s)-2-azanyl-6-[[(3r,4r)-3,4-bis(oxidanyl)-2-oxidanylidene-5-phosphonooxy-pentyl]amino]hexanoic
acid
synonyms:
- (2S)-2-azanyl-6-[[(3R,4R)-3,4-bis(oxidanyl)-2-oxidanylidene-5-phosphonooxy-pentyl]amino]hexanoic
acid
- (2S)-2-amino-6-{[(3R,4R)-3,4-dihydroxy-2-oxo-5-(phosphonooxy)pentyl]amino}hexanoic
acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: L5P
structure: O[C@@H]([C@H](C(=O)C[NH2+]CCCC[C@@H](C(=O)[O-])[NH3+])O)COP(=O)([O-])[O-]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
LA2:
id: LA2
name: n~6~-[(6r)-6,8-disulfanyloctanoyl]-l-lysine
synonyms:
- N~6~-[(6R)-6,8-disulfanyloctanoyl]-L-lysine
- (2S)-2-amino-6-[[(6R)-6,8-bis-sulfanyloctanoyl]amino]hexanoic acid
- K
identifiers:
- ns: pdb-ccd
id: LA2
structure: SCC[C@@H](CCCCC(=O)NCCCC[C@@H](C(=O)[O-])[NH3+])S
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 19
l_bond_atoms:
- molecule: Monomer
element: N
position: 22
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 21
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 22
- molecule: Monomer
element: H
position: 22
charge: 1
LAY:
id: LAY
name: n-acetyl-l-leucine
synonyms:
- N-acetyl-L-leucine
- L
- (2S)-2-acetamido-4-methyl-pentanoic acid
identifiers:
- ns: pdb-ccd
id: LAY
structure: CC(C[C@@H](C(=O)[O-])NC(=O)C)C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
LBY:
id: LBY
name: n~6~-(tert-butoxycarbonyl)-l-lysine
synonyms:
- N~6~-(tert-butoxycarbonyl)-L-lysine
- K
- (2S)-2-azanyl-6-[(2-methylpropan-2-yl)oxycarbonylamino]hexanoic acid
identifiers:
- ns: pdb-ccd
id: LBY
structure: O=C(OC(C)(C)C)NCCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
LCK:
id: LCK
name: (z)-n~6~-(2-carboxy-1-methylethylidene)-l-lysine
synonyms:
- (2S)-2-amino-6-[(4-hydroxy-4-oxo-butan-2-ylidene)amino]hexanoic acid
- (Z)-N~6~-(2-carboxy-1-methylethylidene)-L-lysine
- K
identifiers:
- ns: pdb-ccd
id: LCK
structure: '[O-]C(=O)C/C(=[NH+]\CCCC[C@@H](C(=O)[O-])[NH3+])/C'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
LDH:
id: LDH
name: n~6~-ethyl-l-lysine
synonyms:
- K
- (2S)-2-amino-6-ethylamino-hexanoic acid
- N~6~-ethyl-L-lysine
identifiers:
- ns: pdb-ccd
id: LDH
structure: CC[NH2+]CCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
LE1:
id: LE1
name: 3-sulfanyl-l-valine
synonyms:
- 3-sulfanyl-L-valine
- (2R)-2-amino-3-methyl-3-sulfanyl-butanoic acid
identifiers:
- ns: pdb-ccd
id: LE1
structure: '[NH3+][C@@H](C(S)(C)C)C(=O)[O-]'
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
LEF:
id: LEF
name: (4s)-5-fluoro-l-leucine
synonyms:
- (4S)-5-fluoro-L-leucine
- (2S,4S)-2-amino-5-fluoro-4-methyl-pentanoic acid
- L
identifiers:
- ns: pdb-ccd
id: LEF
structure: FC[C@H](C[C@@H](C(=O)[O-])[NH3+])C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
LEH:
id: LEH
name: n-[12-(1h-imidazol-1-yl)dodecanoyl]-l-leucine
synonyms:
- N-[12-(1H-imidazol-1-yl)dodecanoyl]-L-leucine
- (2S)-2-(12-imidazol-1-yldodecanoylamino)-4-methyl-pentanoic acid
- L
identifiers:
- ns: pdb-ccd
id: LEH
structure: CC(C[C@@H](C(=O)[O-])NC(=O)CCCCCCCCCCCn1ccnc1)C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
LEN:
id: LEN
name: 3-methylbutan-1-amine
synonyms:
- 3-methylbutan-1-amine
- L
identifiers:
- ns: pdb-ccd
id: LEN
structure: '[NH3+]CCC(C)C'
base_monomers:
- L
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
LET:
id: LET
name: (z)-n^6-{3-carboxy-1-[(4-carboxy-2-oxobutoxy)methyl]propylidene}-l-lysine
synonyms:
- (2S)-2-amino-6-[[5-hydroxy-1-(5-hydroxy-2,5-dioxo-pentoxy)-5-oxo-pentan-2-ylidene]amino]hexanoic
acid
- (E)-N~6~-{3-carboxy-1-[(4-carboxy-2-oxobutoxy)methyl]propylidene}-L-lysine
- K
identifiers:
- ns: pdb-ccd
id: LET
structure: '[O-]C(=O)CC/C(=N\CCCC[C@@H](C(=O)[O-])[NH3+])/COCC(=O)CCC(=O)[O-]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
LGY:
id: LGY
name: (e)-n~6~-(4-oxobutylidene)-l-lysine
synonyms:
- (E)-N~6~-(4-oxobutylidene)-L-lysine
- (2S)-2-azanyl-6-[(E)-4-oxobutylideneamino]hexanoic acid
identifiers:
- ns: pdb-ccd
id: LGY
structure: O=CCC/C=[NH+]/CCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
LHC:
id: LHC
name: (2s)-2-amino-4-(4-amino-2-oxopyrimidin-1(2h)-yl)butanoic acid
synonyms:
- (2S)-2-amino-4-(4-amino-2-oxopyrimidin-1(2H)-yl)butanoic acid
- X
- (2S)-2-amino-4-(4-amino-2-oxo-pyrimidin-1-yl)butanoic acid
identifiers:
- ns: pdb-ccd
id: LHC
structure: '[O-]C(=O)[C@@H]([NH3+])CCn1ccc(nc1=O)N'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
LLO:
id: LLO
name: n~6~-[(1s)-3-hydroxy-1,3-dimethylbutyl]-l-lysine
synonyms:
- (2S)-2-azanyl-6-[[(2S)-4-hydroxy-4-methyl-pentan-2-yl]amino]hexanoic acid
- N~6~-[(2S)-4-hydroxy-4-methylpentan-2-yl]-L-lysine
identifiers:
- ns: pdb-ccd
id: LLO
structure: '[O-]C(=O)[C@H](CCCC[NH2+][C@H](CC(O)(C)C)C)[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
LLY:
id: LLY
name: nz-(dicarboxymethyl)lysine
synonyms:
- '{[(5S)-5-amino-5-carboxypentyl]amino}propanedioic acid'
- 2-[[(5S)-5-amino-6-hydroxy-6-oxo-hexyl]amino]propanedioic acid
- K
identifiers:
- ns: pdb-ccd
id: LLY
structure: '[O-]C(=O)[C@H](CCCC[NH2+]C(C(=O)[O-])C(=O)[O-])[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
LLZ:
id: LLZ
name: n~6~-[(1s)-3-(6-methoxynaphthalen-2-yl)-1-methyl-3-oxopropyl]-l-lysine
synonyms:
- N~6~-[(2S)-4-(6-methoxynaphthalen-2-yl)-4-oxobutan-2-yl]-L-lysine
- (2S)-2-azanyl-6-[[(2S)-4-(6-methoxynaphthalen-2-yl)-4-oxo-butan-2-yl]amino]hexanoic
acid
identifiers:
- ns: pdb-ccd
id: LLZ
structure: COc1ccc2c(c1)ccc(c2)C(=O)C[C@@H]([NH2+]CCCC[C@@H](C(=O)[O-])[NH3+])C
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 27
l_bond_atoms:
- molecule: Monomer
element: N
position: 30
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 30
- molecule: Monomer
element: H
position: 30
charge: 1
LME:
id: LME
name: (2s,3r)-2-azanyl-3-methyl-pentanedioic acid
synonyms:
- (2S,3R)-2-azanyl-3-methyl-pentanedioic acid
- E
- (3R)-3-methyl-L-glutamic acid
identifiers:
- ns: pdb-ccd
id: LME
structure: '[O-]C(=O)C[C@H]([C@@H](C(=O)[O-])[NH3+])C'
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
LMQ:
id: LMQ
name: (3s)-3-methyl-l-glutamine
synonyms:
- (3S)-3-methyl-L-glutamine
- Q
- (2S,3S)-2,5-diamino-3-methyl-5-oxo-pentanoic acid
identifiers:
- ns: pdb-ccd
id: LMQ
structure: NC(=O)C[C@@H]([C@@H](C(=O)[O-])[NH3+])C
base_monomers:
- Q
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
LNE:
id: LNE
name: n-ethyl-l-leucinamide
synonyms:
- (2S)-2-azanyl-N-ethyl-4-methyl-pentanamide
- N-ethyl-L-leucinamide
identifiers:
- ns: pdb-ccd
id: LNE
structure: CCNC(=O)[C@H](CC(C)C)[NH3+]
base_monomers:
- L
l_bond_atoms:
- molecule: Monomer
element: N
position: 3
l_displaced_atoms:
- molecule: Monomer
element: H
position: 3
LNM:
id: LNM
name: n-methyl-l-leucinamide
synonyms:
- (2S)-2-azanyl-N,4-dimethyl-pentanamide
- N-methyl-L-leucinamide
identifiers:
- ns: pdb-ccd
id: LNM
structure: CNC(=O)[C@H](CC(C)C)[NH3+]
base_monomers:
- L
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
LP6:
id: LP6
name: 6-piperidin-1-yl-l-norleucine
synonyms:
- 6-piperidin-1-yl-L-norleucine
- K
- (2S)-2-amino-6-piperidin-1-yl-hexanoic acid
identifiers:
- ns: pdb-ccd
id: LP6
structure: '[O-]C(=O)[C@H](CCCC[NH+]1CCCCC1)[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
LPG:
id: LPG
name: l-propargylglycine
synonyms:
- G
- (2S)-2-aminobut-3-ynoic acid
identifiers:
- ns: pdb-ccd
id: LPG
structure: '[O-]C(=O)[C@@H]([NH3+])C#C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
LPH:
id: LPH
name: l-propargylglycine
synonyms:
- (2S)-2-aminopent-4-ynoic acid
- (2S)-2-azanylpent-4-ynoic acid
identifiers:
- ns: pdb-ccd
id: LPH
structure: '[O-]C(=O)[C@@H]([NH3+])CC#C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
LPL:
id: LPL
name: leu-hydroxyethylene-leu
synonyms:
- (2R,4S,5S)-5-amino-4-hydroxy-7-methyl-2-(2-methylpropyl)octanoic acid
- X
identifiers:
- ns: pdb-ccd
id: LPL
structure: CC(C[C@@H]([C@H](C[C@H](C(=O)[O-])CC(C)C)O)[NH3+])C
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
LPS:
id: LPS
name: o-{hydroxy[((2r)-2-hydroxy-3-{[(1s)-1-hydroxypentadecyl]oxy}propyl)oxy]phosphoryl}-l-serine
synonyms:
- S
- (2S)-2-amino-3-[hydroxy-[(2R)-2-hydroxy-3-(1-hydroxypentadecoxy)propoxy]phosphoryl]oxy-propanoic
acid
- O-[(R)-hydroxy{[(2R)-2-hydroxy-3-{[(1R)-1-hydroxypentadecyl]oxy}propyl]oxy}phosphoryl]-L-serine
identifiers:
- ns: pdb-ccd
id: LPS
structure: CCCCCCCCCCCCCCC(OC[C@H](COP(=O)(OC[C@@H](C(=O)[O-])[NH3+])[O-])O)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 28
l_bond_atoms:
- molecule: Monomer
element: N
position: 31
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 31
- molecule: Monomer
element: H
position: 31
charge: 1
LRK:
id: LRK
name: (2s)-2-azanyl-6-[[(2r,4r)-1,4-bis(oxidanyl)-3-oxidanylidene-5-phosphonooxy-pentan-2-yl]amino]hexanoic
acid
synonyms:
- (2S)-2-azanyl-6-[[(2R,4R)-1,4-bis(oxidanyl)-3-oxidanylidene-5-phosphonooxy-pentan-2-yl]amino]hexanoic
acid
- (2S)-2-amino-6-{[(2R,4R)-1,4-dihydroxy-3-oxo-5-(phosphonooxy)pentan-2-yl]amino}hexanoic
acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: LRK
structure: OC[C@H](C(=O)[C@@H](COP(=O)([O-])[O-])O)[NH2+]CCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 25
l_bond_atoms:
- molecule: Monomer
element: N
position: 28
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 28
- molecule: Monomer
element: H
position: 28
charge: 1
LSO:
id: LSO
name: (z)-n~6~-(3-carboxy-1-{[(4-carboxy-2-oxobutyl)sulfonyl]methyl}propylidene)-l-lysine
synonyms:
- (E)-N~6~-(3-carboxy-1-{[(4-carboxy-2-oxobutyl)sulfonyl]methyl}propylidene)-L-lysine
- K
- (2S)-2-amino-6-[[5-hydroxy-1-(5-hydroxy-2,5-dioxo-pentyl)sulfonyl-5-oxo-pentan-2-ylidene]amino]hexanoic
acid
identifiers:
- ns: pdb-ccd
id: LSO
structure: '[O-]C(=O)CC/C(=N\CCCC[C@@H](C(=O)[O-])[NH3+])/CS(=O)(=O)CC(=O)CCC(=O)[O-]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
LTA:
id: LTA
name: 4,8-diamino-3-hydroxy-octanoic acid ethyl ester
synonyms:
- ethyl (3S,4S)-4,8-diamino-3-hydroxyoctanoate
- X
- ethyl (3S,4S)-4,8-diamino-3-hydroxy-octanoate
identifiers:
- ns: pdb-ccd
id: LTA
structure: CCOC(=O)C[C@@H]([C@H](CCCC[NH3+])[NH3+])O
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
LVG:
id: LVG
name: l-vinylglycine
synonyms:
- (2S)-2-aminobut-3-enoic acid
- G
identifiers:
- ns: pdb-ccd
id: LVG
structure: '[O-]C(=O)[C@@H]([NH3+])C=C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
LVN:
id: LVN
name: (3s)-4-oxo-l-valine
synonyms:
- V
- (2S,3S)-2-azanyl-3-methyl-4-oxo-butanoic acid
identifiers:
- ns: pdb-ccd
id: LVN
structure: O=C[C@H]([C@@H](C(=O)[O-])[NH3+])C
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
LWY:
id: LWY
name: 1-[(r)-hydroxy(methyl)phosphoryl]-l-proline
synonyms:
- (2S)-1-[hydroxy(methyl)phosphoryl]pyrrolidine-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: LWY
structure: '[O-]C(=O)[C@@H]1CCCN1P(=O)(C)[O-]'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
LYF:
id: LYF
name: (2e,4s)-2-{[(5s)-5-amino-5-carboxypentyl]imino}-4-hydroxyheptanedioic acid
synonyms:
- (2E,4S)-2-{[(5S)-5-amino-5-carboxypentyl]imino}-4-hydroxyheptanedioic acid
- K
- (2E,4S)-2-[(5S)-5-azanyl-6-oxidanyl-6-oxidanylidene-hexyl]imino-4-oxidanyl-heptanedioic
acid
identifiers:
- ns: pdb-ccd
id: LYF
structure: O[C@H](C/C(=[NH+]\CCCC[C@@H](C(=O)[O-])[NH3+])/C(=O)[O-])CCC(=O)[O-]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
LYH:
id: LYH
name: 3,4 ene-lysine
synonyms:
- (E,2S)-2,6-bis(azanyl)hex-3-enoic acid
- (2S,3E)-2,6-diaminohex-3-enoic acid
identifiers:
- ns: pdb-ccd
id: LYH
structure: '[NH3+]CC/C=C/[C@@H](C(=O)[O-])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
LYO:
id: LYO
name: 4-hydroxy-lysine
synonyms:
- (2S)-2,6-bis(azanyl)-4-hydroxy-hexanoic acid
- K
- (4S)-4-hydroxy-L-lysine
identifiers:
- ns: pdb-ccd
id: LYO
structure: '[O-]C(=O)[C@@H]([NH3+])CC(CC[NH3+])O'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
LYU:
id: LYU
name: n~6~-(4-methylpentyl)-l-lysine
synonyms:
- N~6~-(4-methylpentyl)-L-lysine
- (2S)-2-azanyl-6-(4-methylpentylamino)hexanoic acid
identifiers:
- ns: pdb-ccd
id: LYU
structure: CC(CCC[NH2+]CCCC[C@@H](C(=O)[O-])[NH3+])C
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
LYV:
id: LYV
name: o-phosphono-l-seryl-n-[(3s)-3-amino-3-carboxypropyl]glycinamide
synonyms:
- (2S)-2-azanyl-4-[2-[[(2S)-2-azanyl-3-phosphonooxy-propanoyl]amino]ethanoylamino]butanoic
acid
- O-phosphono-L-seryl-N-[(3S)-3-amino-3-carboxypropyl]glycinamide
identifiers:
- ns: pdb-ccd
id: LYV
structure: O=C(CNC(=O)[C@H](COP(=O)([O-])[O-])[NH3+])NCC[C@@H](C(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 24
l_bond_atoms:
- molecule: Monomer
element: N
position: 27
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 27
- molecule: Monomer
element: H
position: 27
charge: 1
LYX:
id: LYX
name: n''-(2-coenzyme a)-propanoyl-lysine
synonyms:
- (2S)-2-amino-6-[[(2S)-2-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-2-hydroxy-3,3-dimethyl-butanoyl]amino]propanoylamino]ethylsulfanyl]propanoyl]amino]hexanoic
acid
- (3S,5R,9R,19S,26S)-26-amino-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8,19-trimethyl-10,14,20-trioxo-2,4,6-trioxa-18-thia-11,15,21-triaza-3,5-diphosphaheptacosan-27-oic
acid 3,5-dioxide (non-preferred name)
- K
identifiers:
- ns: pdb-ccd
id: LYX
structure: O=C(NCCS[C@H](C(=O)NCCCC[C@@H](C(=O)[O-])[NH3+])C)CCNC(=O)[C@@H](C(COP(=O)(OP(=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1OP(=O)([O-])[O-])O)n1cnc2c1ncnc2N)[O-])[O-])(C)C)O
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
M0H:
id: M0H
name: s-(hydroxymethyl)-l-cysteine
synonyms:
- S-(hydroxymethyl)-L-cysteine
- C
- (2R)-2-amino-3-(hydroxymethylsulfanyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: M0H
structure: '[O-]C(=O)[C@@H]([NH3+])CSCO'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
M2L:
id: M2L
name: (2r)-2-amino-3-(2-dimethylaminoethylsulfanyl)propanoic acid
synonyms:
- S-[2-(dimethylamino)ethyl]-L-cysteine
- K
- (2R)-2-amino-3-(2-dimethylaminoethylsulfanyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: M2L
structure: C[NH+](CCSC[C@@H](C(=O)[O-])[NH3+])C
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
M2S:
id: M2S
name: 3-{[(r)-methylsulfinyl]methyl}-l-valine
synonyms:
- M
- 3-{[(R)-methylsulfinyl]methyl}-L-valine
- (2S)-2-amino-3,3-dimethyl-4-[(R)-methylsulfinyl]butanoic acid
identifiers:
- ns: pdb-ccd
id: M2S
structure: C[S@@](=O)CC([C@@H](C(=O)[O-])[NH3+])(C)C
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
M3R:
id: M3R
name: methyl phosphonated l-arginine
synonyms:
- (2S)-5-carbamimidamido-2-[(hydroxy-methyl-phosphoryl)amino]pentanoic acid
- N~2~-[(R)-hydroxy(methyl)phosphoryl]-L-arginine
identifiers:
- ns: pdb-ccd
id: M3R
structure: '[O-]C(=O)[C@@H](NP(=O)(C)[O-])CCCNC(=[NH2+])N'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
MA:
id: MA
name: methyl l-alaninate
synonyms:
- A
- methyl (2S)-2-aminopropanoate
- methyl L-alaninate
identifiers:
- ns: pdb-ccd
id: MA
structure: COC(=O)[C@@H]([NH3+])C
base_monomers:
- A
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
MBQ:
id: MBQ
name: 2-hydroxy-5-({1-[(4-methylphenoxy)methyl]-3-oxoprop-1-enyl}amino)-l-tyrosine
synonyms:
- (2S)-2-amino-3-[2,4-dihydroxy-5-[[(E)-1-(4-methylphenoxy)-4-oxo-but-2-en-2-yl]amino]phenyl]propanoic
acid
- Y
- 2-hydroxy-5-({(1E)-1-[(4-methylphenoxy)methyl]-3-oxoprop-1-en-1-yl}amino)-L-tyrosine
identifiers:
- ns: pdb-ccd
id: MBQ
structure: O=C/C=C(/Nc1cc(C[C@@H](C(=O)[O-])[NH3+])c(cc1O)O)\COc1ccc(cc1)C
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
MCG:
id: MCG
name: (s)-(alpha)-methyl-4-carboxyphenylglycine
synonyms:
- 4-[(1S)-1-amino-1-carboxyethyl]benzoic acid
- X
- 4-[(2S)-2-amino-1-hydroxy-1-oxo-propan-2-yl]benzoic acid
identifiers:
- ns: pdb-ccd
id: MCG
structure: '[O-]C(=O)c1ccc(cc1)[C@@](C(=O)[O-])([NH3+])C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
MCS:
id: MCS
name: malonyl cysteine
synonyms:
- S-(carboxyacetyl)-L-cysteine
- C
- (2R)-2-amino-3-(3-hydroxy-3-oxo-propanoyl)sulfanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: MCS
structure: '[O-]C(=O)CC(=O)SC[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
MD3:
id: MD3
name: n-(carboxycarbonyl)-s-(naphthalen-2-ylmethyl)-l-cysteine
synonyms:
- N-(carboxycarbonyl)-S-(naphthalen-2-ylmethyl)-L-cysteine
- (2R)-2-(carboxycarbonylamino)-3-(naphthalen-2-ylmethylsulfanyl)propanoic acid
- C
identifiers:
- ns: pdb-ccd
id: MD3
structure: '[O-]C(=O)[C@@H](NC(=O)C(=O)[O-])CSCc1ccc2c(c1)cccc2'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
MD5:
id: MD5
name: n-(carboxycarbonyl)-s-(3-nitrobenzyl)-l-cysteine
synonyms:
- N-(carboxycarbonyl)-S-(3-nitrobenzyl)-L-cysteine
- (2R)-2-(carboxycarbonylamino)-3-[(3-nitrophenyl)methylsulfanyl]propanoic acid
identifiers:
- ns: pdb-ccd
id: MD5
structure: '[O-]C(=O)[C@@H](NC(=O)C(=O)[O-])CSCc1cccc(c1)[N+](=O)[O-]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
MDF:
id: MDF
name: meta, meta'-di-hydroxy-phenylalanine
synonyms:
- methyl (2S)-2-amino-2-(3,5-dihydroxyphenyl)ethanoate
- methyl (2S)-amino(3,5-dihydroxyphenyl)ethanoate
- Y
identifiers:
- ns: pdb-ccd
id: MDF
structure: COC(=O)[C@H](c1cc(O)cc(c1)O)N
base_monomers:
- Y
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
MDO:
id: MDO
name: '{2-[(1s)-1-aminoethyl]-4-methylidene-5-oxo-4,5-dihydro-1h-imidazol-1-yl}acetic
acid'
synonyms:
- 2-[2-[(1S)-1-azanylethyl]-4-methylidene-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
- ASG
- '{2-[(1S)-1-aminoethyl]-4-methylidene-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid'
identifiers:
- ns: pdb-ccd
id: MDO
structure: '[O-]C(=O)CN1C(=O)C(=C)N=C1[C@@H]([NH3+])C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
ME0:
id: ME0
name: hydroxy-l-methionine
synonyms:
- hydroxy-L-methionine
- (2S)-2-azanyl-4-(hydroxymethylsulfanyl)butanoic acid
identifiers:
- ns: pdb-ccd
id: ME0
structure: OCSCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
MEG:
id: MEG
name: (2s,3s)-2-azanyl-3-methyl-pentanedioic acid
synonyms:
- E
- (2S,3S)-2-azanyl-3-methyl-pentanedioic acid
- (3S)-3-methyl-L-glutamic acid
identifiers:
- ns: pdb-ccd
id: MEG
structure: '[O-]C(=O)C[C@@H]([C@@H](C(=O)[O-])[NH3+])C'
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
MF3:
id: MF3
name: 2-amino-4-trifluoromethylsulfanyl-butyric acid
synonyms:
- trifluoro-L-methionine
- X
- (2S)-2-amino-4-(trifluoromethylsulfanyl)butanoic acid
identifiers:
- ns: pdb-ccd
id: MF3
structure: '[O-]C(=O)[C@H](CCSC(F)(F)F)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
MFC:
id: MFC
name: 5-[1-(3-fluoro-4-hydroxy-phenyl)-meth-(z)-ylidene]-3,5-dihydro-imidazol-4-one
synonyms:
- '{(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(3-fluoro-4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid'
- GYG
- 2-[(4Z)-2-[(1R,2R)-1-amino-2-hydroxy-propyl]-4-[(3-fluoro-4-hydroxy-phenyl)methylidene]-5-oxo-imidazol-1-yl]ethanoic
acid
identifiers:
- ns: pdb-ccd
id: MFC
structure: '[O-]C(=O)CN1C(=O)/C(=C/c2ccc(c(c2)F)O)/N=C1[C@H]([C@H](O)C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
MGG:
id: MGG
name: 2-(2-carboxy-acetylamino)-5-guanidino-pentanoic acid
synonyms:
- '[amino-[[(4R)-5-hydroxy-4-[(3-hydroxy-3-oxo-propanoyl)amino]-5-oxo-pentyl]amino]methylidene]azanium'
- R
- amino({(4R)-4-carboxy-4-[(carboxyacetyl)amino]butyl}amino)methaniminium
identifiers:
- ns: pdb-ccd
id: MGG
structure: O=C(N[C@@H](C(=O)[O-])CCCNC(=[NH2+])N)CC(=O)[O-]
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 3
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 3
MH8:
id: MH8
name: (2s)-2-amino-2-methylhept-6-enoic acid
synonyms:
- (2S)-2-azanyl-2-methyl-hept-6-enoic acid
- (2S)-2-amino-2-methylhept-6-enoic acid
identifiers:
- ns: pdb-ccd
id: MH8
structure: C=CCCC[C@@](C(=O)[O-])([NH3+])C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
MHE:
id: MHE
name: 5,5-dimethyl-2-oxohexanoic acid
synonyms:
- 5,5-dimethyl-2-oxo-hexanoic acid
- 5,5-dimethyl-2-oxohexanoic acid
identifiers:
- ns: pdb-ccd
id: MHE
structure: O=C(C(=O)[O-])CCC(C)(C)C
r_bond_atoms:
- molecule: Monomer
element: C
position: 3
r_displaced_atoms:
- molecule: Monomer
element: O
position: 5
charge: -1
MHL:
id: MHL
name: n-methyl-4-hydroxy-leucine
synonyms:
- (2S)-4-hydroxy-4-methyl-2-methylamino-pentanoic acid
- L
- 4-hydroxy-N-methyl-L-leucine
identifiers:
- ns: pdb-ccd
id: MHL
structure: C[NH2+][C@H](C(=O)[O-])CC(O)(C)C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
MHO:
id: MHO
name: s-oxymethionine
synonyms:
- (2S)-2-amino-4-[(S)-methylsulfinyl]butanoic acid
- M
identifiers:
- ns: pdb-ccd
id: MHO
structure: C[S@](=O)CC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
MHU:
id: MHU
name: 4-n,n-(dimethylamino)-l-phenylalanine
synonyms:
- 4-(dimethylamino)-N-methyl-L-phenylalanine
- (2S)-3-(4-dimethylaminophenyl)-2-methylamino-propanoic acid
identifiers:
- ns: pdb-ccd
id: MHU
structure: C[NH2+][C@H](C(=O)[O-])Cc1ccc(cc1)N(C)C
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
MHV:
id: MHV
name: 4-oxo-l-pipecolic acid
synonyms:
- (2S)-4-oxopiperidine-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: MHV
structure: O=C1CC[NH2+][C@@H](C1)C(=O)[O-]
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
MIR:
id: MIR
name: monoethylphosphorylserine
synonyms:
- (2S)-2-amino-3-(ethoxy-hydroxy-phosphoryl)oxy-propanoic acid
- O-[(S)-ethoxy(hydroxy)phosphoryl]-L-serine
identifiers:
- ns: pdb-ccd
id: MIR
structure: '[O-]P(=O)(OCC)OC[C@H]([NH3+])C(=O)[O-]'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
MIS:
id: MIS
name: monoisopropylphosphorylserine
synonyms:
- O-[(R)-hydroxy(1-methylethoxy)phosphoryl]-L-serine
- S
- (2S)-2-amino-3-(hydroxy-propan-2-yloxy-phosphoryl)oxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: MIS
structure: '[NH3+][C@H](C(=O)[O-])COP(=O)(OC(C)C)[O-]'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
MK8:
id: MK8
name: 2-methyl-l-norleucine
synonyms:
- 2-methyl-L-norleucine
- (2S)-2-azanyl-2-methyl-hexanoic acid
- L
identifiers:
- ns: pdb-ccd
id: MK8
structure: '[O-]C(=O)[C@@]([NH3+])(CCCC)C'
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
MKD:
id: MKD
name: (2s)-2-amino-2-methyloctanoic acid
synonyms:
- (2S)-2-azanyl-2-methyl-octanoic acid
- (2S)-2-amino-2-methyloctanoic acid
identifiers:
- ns: pdb-ccd
id: MKD
structure: CCCCCC[C@@](C(=O)[O-])([NH3+])C
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
ML3:
id: ML3
name: 2-{[(2r)-2-amino-2-carboxyethyl]sulfanyl}-n,n,n-trimethylethanaminium
synonyms:
- 2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-N,N,N-trimethylethanaminium
- 2-[(2R)-2-amino-3-hydroxy-3-oxo-propyl]sulfanylethyl-trimethyl-azanium
- K
identifiers:
- ns: pdb-ccd
id: ML3
structure: '[O-]C(=O)[C@H](CSCC[N+](C)(C)C)[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
MMO:
id: MMO
name: n~2~-methyl-l-arginine
synonyms:
- N~2~-methyl-L-arginine
- (2S)-5-carbamimidamido-2-(methylamino)pentanoic acid
- R
identifiers:
- ns: pdb-ccd
id: MMO
structure: C[NH2+][C@H](C(=O)[O-])CCCNC(=[NH2+])N
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
MNL:
id: MNL
name: 4,n-dimethylnorleucine
synonyms:
- (2S,4R)-4-methyl-2-methylamino-hexanoic acid
- (4R)-N,4-dimethyl-L-norleucine
- L
identifiers:
- ns: pdb-ccd
id: MNL
structure: CC[C@H](C[C@@H](C(=O)[O-])[NH2+]C)C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
MOD:
id: MOD
name: l-methionyl adenylate
synonyms:
- '[(2R,3S,4R,5R)-5-(6-amino-1,4-dihydropurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
[(2S)-2-amino-4-methylsulfanyl-butyl] hydrogen phosphate'
- X
- 5'-O-[(S)-{[(2S)-2-amino-4-(methylsulfanyl)butyl]oxy}(hydroxy)phosphoryl]adenosine
identifiers:
- ns: pdb-ccd
id: MOD
structure: CSCC[C@@H](CO[P@@](=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)N1C=NC2=C(NC=NC12)N)[O-])[NH3+]
l_bond_atoms:
- molecule: Monomer
element: N
position: 26
MP4:
id: MP4
name: (2s)-amino(3,5-dihydroxy-4-methylphenyl)ethanoic acid
synonyms:
- (2S)-amino(3,5-dihydroxy-4-methylphenyl)ethanoic acid
- (2S)-2-azanyl-2-[4-methyl-3,5-bis(oxidanyl)phenyl]ethanoic acid
identifiers:
- ns: pdb-ccd
id: MP4
structure: '[NH3+][C@@H](c1cc(O)c(c(c1)O)C)C(=O)[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
MP8:
id: MP8
name: (4r)-4-methyl-l-proline
synonyms:
- P
- (2S,4R)-4-methylpyrrolidine-2-carboxylic acid
- (4R)-4-methyl-L-proline
identifiers:
- ns: pdb-ccd
id: MP8
structure: '[O-]C(=O)[C@@H]1C[C@H](C[NH2+]1)C'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
MPH:
id: MPH
name: (1-amino-3-methylsulfanyl-propyl)-phosphonic acid
synonyms:
- '[(1R)-1-amino-3-(methylsulfanyl)propyl]phosphonic acid'
- '[(1R)-1-amino-3-methylsulfanyl-propyl]phosphonic acid'
- X
identifiers:
- ns: pdb-ccd
id: MPH
structure: CSCC[C@@H](P(=O)([O-])[O-])[NH3+]
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
MPJ:
id: MPJ
name: (1-amino-3-methylsulfanyl-propyl)-phosphinic acid
synonyms:
- (R)-[(1R)-1-amino-3-(methylsulfanyl)propyl]phosphinic acid
- '[(1R)-1-amino-3-methylsulfanyl-propyl]phosphinic acid'
- X
identifiers:
- ns: pdb-ccd
id: MPJ
structure: '[O-]P(=O)[C@@H]([NH3+])CCSC'
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
MPQ:
id: MPQ
name: n-methyl-alpha-phenyl-glycine
synonyms:
- G
- (2S)-2-(methylamino)-2-phenyl-ethanoic acid
- (2S)-(methylamino)(phenyl)ethanoic acid
identifiers:
- ns: pdb-ccd
id: MPQ
structure: '[O-]C(=O)[C@H](c1ccccc1)[NH2+]C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
MSA:
id: MSA
name: (2-s-methyl) sarcosine
synonyms:
- G
- (2R)-(methylamino)(methylsulfanyl)ethanoic acid
- (2R)-2-methylamino-2-methylsulfanyl-ethanoic acid
identifiers:
- ns: pdb-ccd
id: MSA
structure: CS[C@H](C(=O)[O-])[NH2+]C
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
MSE:
id: MSE
name: selenomethionine
synonyms:
- (2S)-2-amino-4-methylselanyl-butanoic acid
- M
- (2S)-2-amino-4-(methylselanyl)butanoic acid
identifiers:
- ns: pdb-ccd
id: MSE
structure: '[O-]C(=O)[C@@H]([NH3+])CC[Se]C'
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
MSL:
id: MSL
name: (2s)-2-amino-4-(methylsulfonimidoyl)butanoic acid
synonyms:
- (2S)-2-amino-4-(S-methylsulfonimidoyl)butanoic acid
- M
- (2S)-2-amino-4-(methylsulfonimidoyl)butanoic acid
identifiers:
- ns: pdb-ccd
id: MSL
structure: '[O-]C(=O)[C@H](CC[S@](=O)(=N)C)[NH3+]'
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
MSO:
id: MSO
name: selenomethionine selenoxide
synonyms:
- (2S)-2-amino-4-[(R)-methylseleninyl]butanoic acid
- (2S)-2-amino-4-(methylseleninyl)butanoic acid
- M
identifiers:
- ns: pdb-ccd
id: MSO
structure: C[Se](=O)CC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
MSP:
id: MSP
name: 5'-o-[(l-methionyl)-sulphamoyl]adenosine
synonyms:
- 5'-O-(L-methionylsulfamoyl)adenosine
- '[(2R,3S,4R,5R)-5-(6-amino-1,4-dihydropurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
N-[(2S)-2-amino-4-methylsulfanyl-butanoyl]sulfamate'
- X
identifiers:
- ns: pdb-ccd
id: MSP
structure: CSCC[C@@H](C(=O)[N-]S(=O)(=O)OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)N1C=NC2=C(NC=NC12)N)N
l_bond_atoms:
- molecule: Monomer
element: N
position: 28
MT2:
id: MT2
name: '[(3s)-3-amino-3-carboxypropyl](ethyl)methylsulfonium'
synonyms:
- M
- '[(3S)-3-amino-3-carboxypropyl](ethyl)methylsulfonium'
- '[(3S)-3-amino-4-hydroxy-4-oxo-butyl]-ethyl-methyl-sulfanium'
identifiers:
- ns: pdb-ccd
id: MT2
structure: CC[S@+](CC[C@@H](C(=O)[O-])[NH3+])C
base_monomers:
- M
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
MTY:
id: MTY
name: meta-tyrosine
synonyms:
- 3-hydroxy-L-phenylalanine
- Y
- (2S)-2-amino-3-(3-hydroxyphenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: MTY
structure: '[O-]C(=O)[C@H](Cc1cccc(c1)O)[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
MVA:
id: MVA
name: n-methylvaline
synonyms:
- V
- N-methyl-L-valine
- (2S)-3-methyl-2-(methylamino)butanoic acid
identifiers:
- ns: pdb-ccd
id: MVA
structure: C[NH2+][C@H](C(=O)[O-])C(C)C
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
MYN:
id: MYN
name: (2s)-amino[(4r)-2-amino-1,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid
synonyms:
- (2S)-2-azanyl-2-[(4R)-2-azanyl-1,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid
identifiers:
- ns: pdb-ccd
id: MYN
structure: '[O-]C(=O)[C@H]([C@H]1CCNC(=[NH+]1)N)N'
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
N10:
id: N10
name: o-[(hexylamino)carbonyl]-l-serine
synonyms:
- S
- (2S)-2-amino-3-(hexylcarbamoyloxy)propanoic acid
- O-(hexylcarbamoyl)-L-serine
identifiers:
- ns: pdb-ccd
id: N10
structure: CCCCCCNC(=O)OC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
N2C:
id: N2C
name: n,s-dimethylcysteine
synonyms:
- N,S-dimethyl-L-cysteine
- (2R)-2-methylamino-3-methylsulfanyl-propanoic acid
- X
identifiers:
- ns: pdb-ccd
id: N2C
structure: CSC[C@@H](C(=O)[O-])[NH2+]C
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
N7P:
id: N7P
name: 1-acetyl-l-proline
synonyms:
- P
- (2~{S})-1-ethanoylpyrrolidine-2-carboxylic acid
- 1-acetyl-L-proline
identifiers:
- ns: pdb-ccd
id: N7P
structure: CC(=O)N1CCC[C@H]1C(=O)[O-]
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
N80:
id: N80
name: 1-ethenyl-l-proline
synonyms:
- 1-ethenyl-L-proline
- P
- (2S)-1-ethenylpyrrolidine-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: N80
structure: C=C[NH+]1CCC[C@H]1C(=O)[O-]
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
NA8:
id: NA8
name: (1s)-1-carboxy-2-naphthalen-2-ylethanaminium
synonyms:
- A
- (1S)-1-carboxy-2-naphthalen-2-ylethanaminium
- '[(2S)-1-hydroxy-3-naphthalen-2-yl-1-oxo-propan-2-yl]azanium'
identifiers:
- ns: pdb-ccd
id: NA8
structure: '[O-]C(=O)[C@H](Cc1ccc2c(c1)cccc2)[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
NAL:
id: NAL
name: beta-(2-naphthyl)-alanine
synonyms:
- A
- (2S)-2-azanyl-3-naphthalen-2-yl-propanoic acid
- (2S)-2-amino-3-(naphthalen-2-yl)propanoic acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: NAL
structure: '[O-]C(=O)[C@H](Cc1ccc2c(c1)cccc2)[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
NB8:
id: NB8
name: 5'-o-[(r)-{[(2s)-2-amino-4-(hydroxyamino)-4-oxobutanoyl]oxy}(hydroxy)phosphoryl]adenosine
synonyms:
- N
- 5'-O-[(R)-{[(2S)-2-amino-4-(hydroxyamino)-4-oxobutanoyl]oxy}(hydroxy)phosphoryl]adenosine
- '[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]
(2S)-2-amino-4-(hydroxyamino)-4-oxo-butanoate'
identifiers:
- ns: pdb-ccd
id: NB8
structure: ONC(=O)C[C@@H](C(=O)OP(=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)[O-])N
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
NBQ:
id: NBQ
name: 2-hydroxy-5-({1-[(2-naphthyloxy)methyl]-3-oxoprop-1-enyl}amino)tyrosine
synonyms:
- 2-hydroxy-5-({(1E)-1-[(naphthalen-2-yloxy)methyl]-3-oxoprop-1-en-1-yl}amino)-L-tyrosine
- Y
- (2S)-2-amino-3-[2,4-dihydroxy-5-[[(E)-1-naphthalen-2-yloxy-4-oxo-but-2-en-2-yl]amino]phenyl]propanoic
acid
identifiers:
- ns: pdb-ccd
id: NBQ
structure: O=C/C=C(/Nc1cc(C[C@@H](C(=O)[O-])[NH3+])c(cc1O)O)\COc1ccc2c(c1)cccc2
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
NC1:
id: NC1
name: nitrocefin acyl-serine
synonyms:
- (2R)-2-[(1R)-2-[(2S)-2-amino-3-oxido-3-oxo-propoxy]-2-oxo-1-(2-thiophen-2-ylethanoylamino)ethyl]-5-[(E)-2-(2,4-dinitrophenyl)ethenyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylate
- S
- (2R)-2-{(1R)-2-[(2S)-2-amino-2-carboxylatoethoxy]-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5-[(E)-2-(2,4-dinitrophenyl)ethenyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylate
identifiers:
- ns: pdb-ccd
id: NC1
structure: O=C(N[C@@H]([C@H]1SCC(=C([NH2+]1)C(=O)[O-])/C=C/c1ccc(cc1[N+](=O)[O-])[N+](=O)[O-])C(=O)OC[C@@H](C(=O)[O-])[NH3+])Cc1cccs1
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
NCB:
id: NCB
name: n-carbamoyl-alanine
synonyms:
- A
- N-carbamoyl-D-alanine
- (2R)-2-(aminocarbonylamino)propanoic acid
identifiers:
- ns: pdb-ccd
id: NCB
structure: NC(=O)N[C@@H](C(=O)[O-])C
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
NCY:
id: NCY
name: n-methylcysteine
synonyms:
- (2R)-2-methylamino-3-sulfanyl-propanoic acid
- X
- N-methyl-L-cysteine
identifiers:
- ns: pdb-ccd
id: NCY
structure: '[O-]C(=O)[C@@H]([NH2+]C)CS'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
NKS:
id: NKS
name: n-(3-{[2-(4-chlorophenyl)-5-methyl-1,3-oxazol-4-yl]methoxy}benzyl)-n-[(4-methylphenoxy)carbonyl]glycine
synonyms:
- N-(3-{[2-(4-chlorophenyl)-5-methyl-1,3-oxazol-4-yl]methoxy}benzyl)-N-[(4-methylphenoxy)carbonyl]glycine
- 2-[[3-[[2-(4-chlorophenyl)-5-methyl-1,3-oxazol-4-yl]methoxy]phenyl]methyl-(4-methylphenoxy)carbonyl-amino]ethanoic
acid
identifiers:
- ns: pdb-ccd
id: NKS
structure: '[O-]C(=O)CN(C(=O)Oc1ccc(cc1)C)Cc1cccc(c1)OCc1nc(oc1C)c1ccc(cc1)Cl'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 26
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
NLB:
id: NLB
name: 6-(benzyloxy)-l-norleucine
synonyms:
- (2S)-2-azanyl-6-phenylmethoxy-hexanoic acid
- 6-(benzyloxy)-L-norleucine
identifiers:
- ns: pdb-ccd
id: NLB
structure: '[O-]C(=O)[C@H](CCCCOCc1ccccc1)[NH3+]'
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
NLE:
id: NLE
name: norleucine
synonyms:
- L-norleucine
- (2S)-2-aminohexanoic acid
- L
identifiers:
- ns: pdb-ccd
id: NLE
structure: '[O-]C(=O)[C@@H]([NH3+])CCCC'
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
NLN:
id: NLN
name: norleucine amide
synonyms:
- L-norleucinamide
- (2S)-2-aminohexanamide
- L
identifiers:
- ns: pdb-ccd
id: NLN
structure: CCCC[C@H]([NH3+])C(=O)N
base_monomers:
- L
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
- molecule: Monomer
element: H
position: 7
charge: 1
NLO:
id: NLO
name: o-methyl-l-norleucine
synonyms:
- methyl (2S)-2-aminohexanoate
- L
- methyl L-norleucinate
identifiers:
- ns: pdb-ccd
id: NLO
structure: CCCC[C@@H](C(=O)OC)[NH3+]
base_monomers:
- L
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
NLP:
id: NLP
name: (1-amino-pentyl)-phosphonic acid
synonyms:
- '[(1R)-1-aminopentyl]phosphonic acid'
- L
identifiers:
- ns: pdb-ccd
id: NLP
structure: CCCC[C@@H](P(=O)([O-])[O-])[NH3+]
base_monomers:
- L
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
NLQ:
id: NLQ
name: n~2~-acetyl-l-glutamine
synonyms:
- N~2~-acetyl-L-glutamine
- Q
- (2S)-2-acetamido-5-amino-5-oxo-pentanoic acid
identifiers:
- ns: pdb-ccd
id: NLQ
structure: NC(=O)CC[C@@H](C(=O)[O-])NC(=O)C
base_monomers:
- Q
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
NMC:
id: NMC
name: n-cyclopropylmethyl glycine
synonyms:
- G
- 2-(cyclopropylmethylamino)ethanoic acid
- N-(cyclopropylmethyl)glycine
identifiers:
- ns: pdb-ccd
id: NMC
structure: '[O-]C(=O)C[NH2+]CC1CC1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
- molecule: Monomer
element: H
position: 5
charge: 1
NMM:
id: NMM
name: (2s)-2-amino-5-[(n-methylcarbamimidoyl)amino]pentanoic acid
synonyms:
- N~5~-(N-methylcarbamimidoyl)-L-ornithine
- R
- (2S)-2-amino-5-[(N-methylcarbamimidoyl)amino]pentanoic acid
identifiers:
- ns: pdb-ccd
id: NMM
structure: CNC(=[NH2+])NCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
NNH:
id: NNH
name: nor-n-omega-hydroxy-l-arginine
synonyms:
- (2S)-2-amino-4-[(N-hydroxycarbamimidoyl)amino]butanoic acid
- R
- (2S)-2-amino-4-(N'-hydroxycarbamimidamido)butanoic acid
identifiers:
- ns: pdb-ccd
id: NNH
structure: '[O-]C(=O)[C@@H]([NH3+])CCNC(=[NH2+])NO'
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
NOT:
id: NOT
name: 6-azido-l-norleucine
synonyms:
- (2S)-2-amino-6-azido-hexanoic acid
- 6-azido-L-norleucine
identifiers:
- ns: pdb-ccd
id: NOT
structure: '[N-]=[N+]=NCCCC[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
NPH:
id: NPH
name: cysteine-methylene-carbamoyl-1,10-phenanthroline
synonyms:
- (2R)-2-amino-3-[2-oxo-2-(1,10-phenanthrolin-5-ylamino)ethyl]sulfanyl-propanoic
acid
- S-[2-oxo-2-(1,10-phenanthrolin-5-ylamino)ethyl]-L-cysteine
- C
identifiers:
- ns: pdb-ccd
id: NPH
structure: O=C(Nc1cc2cccnc2c2c1cccn2)CSC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 23
l_bond_atoms:
- molecule: Monomer
element: N
position: 26
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 26
- molecule: Monomer
element: H
position: 26
charge: 1
NPI:
id: NPI
name: (2s)-2-aminoheptanedioic acid
synonyms:
- A
- (2S)-2-aminoheptanedioic acid
- (2S)-2-azanylheptanedioic acid
identifiers:
- ns: pdb-ccd
id: NPI
structure: '[O-]C(=O)CCCC[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
NRG:
id: NRG
name: n-omega-nitro-l-arginine
synonyms:
- N~5~-(N-nitrocarbamimidoyl)-L-ornithine
- (2S)-2-amino-5-[(N-nitrocarbamimidoyl)amino]pentanoic acid
identifiers:
- ns: pdb-ccd
id: NRG
structure: '[O-][N+](=O)NC(=[NH2+])NCCC[C@@H](C(=O)[O-])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
NRP:
id: NRP
name: '{4-[(4-hydroxyphenyl)methylidene]-2-[(1e)-3-methylbutanimidoyl]-5-oxo-4,5-dihydro-1h-imidazol-1-yl}acetic
acid'
synonyms:
- 2-[4-[(4-hydroxyphenyl)methylidene]-2-(3-methylbutanimidoyl)-5-oxo-imidazol-1-yl]ethanoic
acid
- '{(4E)-4-(4-hydroxybenzylidene)-2-[(1E)-3-methylbutanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid'
- LYG
identifiers:
- ns: pdb-ccd
id: NRP
structure: CC(CC(=N)C1=NC(=Cc2ccc(cc2)O)C(=O)N1CC(=O)[O-])C
r_bond_atoms:
- molecule: Monomer
element: C
position: 21
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
NSK:
id: NSK
name: n-succinyl lysine
synonyms:
- X
- (2S)-6-amino-2-[(4-hydroxy-4-oxo-butanoyl)amino]hexanoic acid
- N~2~-(3-carboxypropanoyl)-L-lysine
identifiers:
- ns: pdb-ccd
id: NSK
structure: '[NH3+]CCCC[C@@H](C(=O)[O-])NC(=O)CCC(=O)[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
NTR:
id: NTR
name: meta-hydroxy beta nor-tyrosine
synonyms:
- (2R)-2-amino-2-(3,4-dihydroxyphenyl)ethanoic acid
- Y
- (2R)-amino(3,4-dihydroxyphenyl)ethanoic acid
identifiers:
- ns: pdb-ccd
id: NTR
structure: '[O-]C(=O)[C@@H](c1ccc(c(c1)O)O)[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
NVA:
id: NVA
name: norvaline
synonyms:
- V
- (2S)-2-aminopentanoic acid
- L-norvaline
identifiers:
- ns: pdb-ccd
id: NVA
structure: '[O-]C(=O)[C@@H]([NH3+])CCC'
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
NWD:
id: NWD
name: 3-(5-nitro-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-l-alanine
synonyms:
- (2S)-2-azanyl-3-[5-nitro-2,4-bis(oxidanylidene)pyrimidin-1-yl]propanoic acid
- 3-(5-nitro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine
identifiers:
- ns: pdb-ccd
id: NWD
structure: '[O-]C(=O)[C@H](CN1CC([N+](=O)[O-])C(=O)[N-]C1=O)[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
NYB:
id: NYB
name: n-methyl-s-[(1r)-1-methylpropyl]-l-cysteine
synonyms:
- (2R)-3-[(2R)-butan-2-yl]sulfanyl-2-methylamino-propanoic acid
- N-methyl-S-[(1R)-1-methylpropyl]-L-cysteine
identifiers:
- ns: pdb-ccd
id: NYB
structure: CC[C@H](SC[C@@H](C(=O)[O-])[NH2+]C)C
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
NYS:
id: NYS
name: s-{5-[(1r)-2-amino-1-hydroxyethyl]-2,3-dihydroxyphenyl}-l-cysteine
synonyms:
- (2R)-2-amino-3-[5-[(1R)-2-amino-1-hydroxy-ethyl]-2,3-dihydroxy-phenyl]sulfanyl-propanoic
acid
- S-{5-[(1R)-2-amino-1-hydroxyethyl]-2,3-dihydroxyphenyl}-L-cysteine
- C
identifiers:
- ns: pdb-ccd
id: NYS
structure: '[NH3+]C[C@@H](c1cc(SC[C@@H](C(=O)[O-])[NH3+])c(c(c1)O)O)O'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
NZC:
id: NZC
name: n-methylidene-l-threonine
synonyms:
- (2S,3R)-2-(methylamino)-3-oxidanyl-butanoic acid
- T
- N-methyl-L-threonine
identifiers:
- ns: pdb-ccd
id: NZC
structure: C[NH2+][C@H](C(=O)[O-])[C@H](O)C
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
NZH:
id: NZH
name: (2s)-2-amino-3-[1-(1h-tetraazol-5-yl)-1h-imidazol-4-yl]propanal
synonyms:
- (2S)-2-amino-3-[1-(1H-1,2,3,4-tetrazol-5-yl)imidazol-4-yl]propanal
- H
- (2S)-2-amino-3-[1-(1H-tetrazol-5-yl)-1H-imidazol-4-yl]propanal
identifiers:
- ns: pdb-ccd
id: NZH
structure: '[O-]C(=O)[C@H](Cc1ncn(c1)c1[n-]nnn1)[NH3+]'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
O12:
id: O12
name: n~5~-dodecanoyl-l-ornithine
synonyms:
- (2S)-2-amino-5-(dodecanoylamino)pentanoic acid
- X
- N~5~-dodecanoyl-L-ornithine
identifiers:
- ns: pdb-ccd
id: O12
structure: CCCCCCCCCCCC(=O)NCCC[C@@H](C(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 23
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 23
- molecule: Monomer
element: H
position: 23
charge: 1
OBF:
id: OBF
name: (2s)-2-amino-4,4-difluorobutanoic acid
synonyms:
- (2S)-2-amino-4,4-difluorobutanoic acid
- (2S)-2-amino-4,4-difluoro-butanoic acid
- X
identifiers:
- ns: pdb-ccd
id: OBF
structure: '[NH3+][C@H](C(=O)[O-])CC(F)F'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
OBS:
id: OBS
name: (z)-n^6-[(4s,5r)-5-(2-carboxyethyl)-4-(carboxymethyl)-1-hydroxydihydro-2h-thiopyranium-3(4h)-ylidene]-l-lysine
synonyms:
- (E)-N~6~-[(1S,4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)-1-oxidodihydro-2H-thiopyran-3(4H)-ylidene]-L-lysine
- K
- (2S)-2-amino-6-[[(1S,4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)-1-oxo-thian-3-ylidene]amino]hexanoic
acid
identifiers:
- ns: pdb-ccd
id: OBS
structure: '[O-]C(=O)C[C@@H]1[C@H](CCC(=O)[O-])C[S@](=O)C/C/1=N/CCCC[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 26
l_bond_atoms:
- molecule: Monomer
element: N
position: 29
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 29
- molecule: Monomer
element: H
position: 29
charge: 1
OCY:
id: OCY
name: hydroxyethylcysteine
synonyms:
- (2R)-2-amino-3-(2-hydroxyethylsulfanyl)propanoic acid
- C
- S-(2-hydroxyethyl)-L-cysteine
identifiers:
- ns: pdb-ccd
id: OCY
structure: '[O-]C(=O)[C@@H]([NH3+])CSCCO'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
OFM:
id: OFM
name: '[(4z)-2-{(2r,5r)-2-[(1s)-1-amino-2-phenylethyl]-2-hydroxy-5-methyl-2,5-dihydro-1,3-oxazol-4-yl}-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic
acid'
synonyms:
- '[(4Z)-2-{(2R,5R)-2-[(1S)-1-amino-2-phenylethyl]-2-hydroxy-5-methyl-2,5-dihydro-1,3-oxazol-4-yl}-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic
acid'
- 2-[(4Z)-2-[(2R,5R)-2-[(1S)-1-azanyl-2-phenyl-ethyl]-5-methyl-2-oxidanyl-5H-1,3-oxazol-4-yl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
identifiers:
- ns: pdb-ccd
id: OFM
structure: '[O-]C(=O)CN1C(=N/C(=C\c2ccc(cc2)O)/C1=O)C1=N[C@@](O[C@@H]1C)(O)[C@H](Cc1ccccc1)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
OHI:
id: OHI
name: 3-(2-oxo-2h-imidazol-4-yl)-l-alanine
synonyms:
- 3-(2-oxo-2H-imidazol-4-yl)-L-alanine
- H
- (2S)-2-amino-3-(2-oxoimidazol-4-yl)propanoic acid
identifiers:
- ns: pdb-ccd
id: OHI
structure: '[O-]C(=O)[C@H](CC1=NC(=O)N=C1)[NH3+]'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
OIC:
id: OIC
name: octahydroindole-2-carboxylic acid
synonyms:
- (2S,3aS,7aS)-2,3,3a,4,5,6,7,7a-octahydro-1H-indole-2-carboxylic acid
- X
- (2S,3aS,7aS)-octahydro-1H-indole-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: OIC
structure: '[O-]C(=O)[C@@H]1C[C@H]2[C@@H]([NH2+]1)CCCC2'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
OIM:
id: OIM
name: '[(4z)-2-{(2r,5r)-2-[(1s,2s)-1-amino-2-methylbutyl]-2-hydroxy-5-methyl-2,5-dihydro-1,3-oxazol-4-yl}-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic
acid'
synonyms:
- 2-[(4Z)-2-[(2R,5R)-2-[(1S,2S)-1-azanyl-2-methyl-butyl]-5-methyl-2-oxidanyl-5H-1,3-oxazol-4-yl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
- '[(4Z)-2-{(2R,5R)-2-[(1S,2S)-1-amino-2-methylbutyl]-2-hydroxy-5-methyl-2,5-dihydro-1,3-oxazol-4-yl}-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic
acid'
identifiers:
- ns: pdb-ccd
id: OIM
structure: CC[C@@H]([C@@H]([C@]1(O)N=C([C@H](O1)C)C1=N/C(=C\c2ccc(cc2)O)/C(=O)N1CC(=O)[O-])[NH3+])C
r_bond_atoms:
- molecule: Monomer
element: C
position: 30
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 32
charge: -1
OLD:
id: OLD
name: 3-[2-(4-bromophenyl)-2-oxoethyl]-l-histidine
synonyms:
- 3-[2-(4-bromophenyl)-2-oxoethyl]-L-histidine
- (2S)-2-amino-3-[3-[2-(4-bromophenyl)-2-oxo-ethyl]imidazol-4-yl]propanoic acid
identifiers:
- ns: pdb-ccd
id: OLD
structure: '[O-]C(=O)[C@H](Cc1cncn1CC(=O)c1ccc(cc1)Br)[NH3+]'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 22
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 22
- molecule: Monomer
element: H
position: 22
charge: 1
OLZ:
id: OLZ
name: o-(2-aminoethyl)-l-serine
synonyms:
- S
- (2S)-2-amino-3-(2-aminoethoxy)propanoic acid
- O-(2-aminoethyl)-L-serine
identifiers:
- ns: pdb-ccd
id: OLZ
structure: '[O-]C(=O)[C@@H]([NH3+])COCC[NH3+]'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
OMH:
id: OMH
name: o-[(s)-hydroxy(methoxy)phosphoryl]-l-serine
synonyms:
- (2S)-2-amino-3-(hydroxy-methoxy-phosphoryl)oxy-propanoic acid
- O-[(S)-hydroxy(methoxy)phosphoryl]-L-serine
identifiers:
- ns: pdb-ccd
id: OMH
structure: '[O-]P(=O)(OC)OC[C@H]([NH3+])C(=O)[O-]'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
OMX:
id: OMX
name: (betar)-beta-hydroxy-l-tyrosine
synonyms:
- (2S,3R)-2-azanyl-3-(4-hydroxyphenyl)-3-oxidanyl-propanoic acid
- Y
- (betaR)-beta-hydroxy-L-tyrosine
identifiers:
- ns: pdb-ccd
id: OMX
structure: O[C@@H]([C@@H](C(=O)[O-])[NH3+])c1ccc(cc1)O
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
OMY:
id: OMY
name: (betar)-3-chloro-beta-hydroxy-l-tyrosine
synonyms:
- (betaR)-3-chloro-beta-hydroxy-L-tyrosine
- Y
- (2S,3R)-2-amino-3-(3-chloro-4-hydroxy-phenyl)-3-hydroxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: OMY
structure: '[O-]C(=O)[C@H]([C@@H](c1ccc(c(c1)Cl)O)O)[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
ONH:
id: ONH
name: n~5~-hydroxy-l-ornithine
synonyms:
- A
- (2S)-2-azanyl-5-(oxidanylamino)pentanoic acid
- N~5~-hydroxy-L-ornithine
identifiers:
- ns: pdb-ccd
id: ONH
structure: ONCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
ONL:
id: ONL
name: 5-oxo-l-norleucine
synonyms:
- 5-oxo-L-norleucine
- X
- (2S)-2-amino-5-oxo-hexanoic acid
identifiers:
- ns: pdb-ccd
id: ONL
structure: CC(=O)CC[C@@H](C(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
ORN:
id: ORN
name: l-ornithine
synonyms:
- A
- (2S)-2,5-bis(azanyl)pentanoic acid
- L-ornithine
identifiers:
- ns: pdb-ccd
id: ORN
structure: '[O-]C(=O)[C@@H]([NH3+])CCC[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
ORQ:
id: ORQ
name: n~5~-acetyl-l-ornithine
synonyms:
- N~5~-acetyl-L-ornithine
- (2S)-5-acetamido-2-amino-pentanoic acid
- R
identifiers:
- ns: pdb-ccd
id: ORQ
structure: CC(=O)NCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
OTH:
id: OTH
name: n,o-dimethyl-l-threonine
synonyms:
- N,O-dimethyl-L-threonine
- T
- (2S,3R)-3-methoxy-2-(methylamino)butanoic acid
identifiers:
- ns: pdb-ccd
id: OTH
structure: CO[C@@H]([C@@H](C(=O)[O-])[NH2+]C)C
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
OTY:
id: OTY
name: 2-hydroxy-l-tyrosine
synonyms:
- (2S)-2-azanyl-3-[2,4-bis(oxidanyl)phenyl]propanoic acid
- 2-hydroxy-L-tyrosine
identifiers:
- ns: pdb-ccd
id: OTY
structure: '[O-]C(=O)[C@H](Cc1ccc(cc1O)O)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
OXX:
id: OXX
name: oxalyl-aspartyl anhydride
synonyms:
- D
- 2-[(3S)-3-amino-4-hydroxy-4-oxo-butanoyl]oxy-2-oxo-ethanoate
- '{[(3S)-3-amino-3-carboxypropanoyl]oxy}(oxo)acetate (non-preferred name)'
identifiers:
- ns: pdb-ccd
id: OXX
structure: O=C(OC(=O)C(=O)[O-])C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
OYL:
id: OYL
name: 1-ethyl-l-histidine
synonyms:
- 1-ethyl-L-histidine
- (2S)-2-azanyl-3-(1-ethylimidazol-4-yl)propanoic acid
identifiers:
- ns: pdb-ccd
id: OYL
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1cn(cn1)CC'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
OZT:
id: OZT
name: (4s,5r)-5-methyl-2-oxo-1,3-oxazolidine-4-carboxylic acid
synonyms:
- (4S,5R)-5-methyl-2-oxo-1,3-oxazolidine-4-carboxylic acid
identifiers:
- ns: pdb-ccd
id: OZT
structure: O=C1O[C@@H]([C@H](N1)C(=O)[O-])C
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
P2Q:
id: P2Q
name: 2-hydroxy-5-{[(1s,2e)-1-formyl-4-phenoxybut-2-en-1yl]amino}-l-tyrosine
synonyms:
- (2S)-2-azanyl-3-[2,4-dihydroxy-5-[[(E,2S)-1-oxo-5-phenoxy-pent-3-en-2-yl]amino]phenyl]propanoic
acid
identifiers:
- ns: pdb-ccd
id: P2Q
structure: O=C[C@@H](Nc1cc(C[C@@H](C(=O)[O-])[NH3+])c(cc1O)O)/C=C/COc1ccccc1
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
P2Y:
id: P2Y
name: (2s)-pyrrolidin-2-ylmethylamine
synonyms:
- P
- 1-[(2S)-pyrrolidin-2-yl]methanamine
- '[(2S)-pyrrolidin-2-yl]methanamine'
identifiers:
- ns: pdb-ccd
id: P2Y
structure: '[NH3+]C[C@@H]1CCC[NH2+]1'
base_monomers:
- P
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
P3Q:
id: P3Q
name: 2-hydroxy-5-{[(1e)-1-(2-oxoethylidene)-4-phenylbutyl]amino}-l-tyrosine
synonyms:
- (2S)-2-azanyl-3-[2,4-dihydroxy-5-[[(E)-1-oxo-6-phenyl-hex-2-en-3-yl]amino]phenyl]propanoic
acid
identifiers:
- ns: pdb-ccd
id: P3Q
structure: O=C/C=C(/Nc1cc(C[C@@H](C(=O)[O-])[NH3+])c(cc1O)O)\CCCc1ccccc1
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
P4E:
id: P4E
name: (2s,4e)-2-amino-5-phenylpent-4-enoic acid
synonyms:
- (2S)-2-azanyl-5-phenyl-pent-4-enoic acid
- (2S,4E)-2-amino-5-phenylpent-4-enoic acid
identifiers:
- ns: pdb-ccd
id: P4E
structure: '[O-]C(=O)[C@H](CC=Cc1ccccc1)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
P9S:
id: P9S
name: dihydroxypropylcysteine
synonyms:
- C
- (2~{R})-2-azanyl-3-[(2~{R})-2,3-bis(oxidanyl)propyl]sulfanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: P9S
structure: OC[C@H](CSC[C@@H](C(=O)[O-])[NH3+])O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
PAQ:
id: PAQ
name: 2-oxy-4-hydroxy-5-(2-hydrazinopyridine)phenylalanine
synonyms:
- 3-[(1R)-4-hydroxy-6-oxo-3-(2-pyridin-2-ylhydrazino)cyclohexa-2,4-dien-1-yl]-L-alanine
- (2S)-2-amino-3-[4-hydroxy-6-oxo-3-(2-pyridin-2-ylhydrazinyl)-1-cyclohexa-2,4-dienyl]propanoic
acid
- Y
identifiers:
- ns: pdb-ccd
id: PAQ
structure: '[O-]C(=O)[C@H](C[C-]1C=C([NH2+]Nc2cccc[nH+]2)C(=CC1=O)[O-])[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 26
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 26
- molecule: Monomer
element: H
position: 26
charge: 1
PAT:
id: PAT
name: alpha-phosphono-tryptophan
synonyms:
- (2R)-2-amino-3-(1H-indol-3-yl)-2-phosphono-propanoic acid
- alpha-phosphono-L-tryptophan
- W
identifiers:
- ns: pdb-ccd
id: PAT
structure: '[O-]C(=O)[C@](P(=O)([O-])[O-])(Cc1c[nH]c2c1cccc2)[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
PBB:
id: PBB
name: s-(4-bromobenzyl)cysteine
synonyms:
- (2R)-2-amino-3-[(4-bromophenyl)methylsulfanyl]propanoic acid
- C
- S-(4-bromobenzyl)-L-cysteine
identifiers:
- ns: pdb-ccd
id: PBB
structure: '[NH3+][C@H](C(=O)[O-])CSCc1ccc(cc1)Br'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
PBF:
id: PBF
name: para-(benzoyl)-phenylalanine
synonyms:
- F
- 4-(phenylcarbonyl)-L-phenylalanine
- (2S)-2-amino-3-[4-(phenylcarbonyl)phenyl]propanoic acid
identifiers:
- ns: pdb-ccd
id: PBF
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)C(=O)c1ccccc1'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
PCE:
id: PCE
name: 2-(3-amino-4-cyclohexyl-2-hydroxy-butyl)-pent-4-ynoic acid
synonyms:
- (2R,4R,5S)-5-amino-6-cyclohexyl-4-hydroxy-2-prop-2-yn-1-ylhexanoic acid
- X
- (4R,5S)-5-amino-6-cyclohexyl-4-hydroxy-2-prop-2-ynyl-hexanoic acid
identifiers:
- ns: pdb-ccd
id: PCE
structure: C#CCC(C(=O)[O-])C[C@H]([C@H](CC1CCCCC1)[NH3+])O
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
PCS:
id: PCS
name: phenylalanylmethylchloride
synonyms:
- F
- (3S)-3-amino-1-chloro-4-phenyl-butan-2-one
- (3S)-3-amino-1-chloro-4-phenylbutan-2-one
identifiers:
- ns: pdb-ccd
id: PCS
structure: ClCC(=O)[C@H](Cc1ccccc1)[NH3+]
base_monomers:
- F
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
PE1:
id: PE1
name: n~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-l-lysine
synonyms:
- N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-lysine
- (2S)-6-azanyl-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]hexanoic
acid
- K
identifiers:
- ns: pdb-ccd
id: PE1
structure: '[NH3+]CCCC[C@@H](C(=O)[O-])[NH2+]Cc1c(cnc(c1O)C)COP(=O)([O-])[O-]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
PEC:
id: PEC
name: s,s-pentylthiocysteine
synonyms:
- (2R)-2-amino-3-pentyldisulfanyl-propanoic acid
- 3-(pentyldisulfanyl)-L-alanine
- C
identifiers:
- ns: pdb-ccd
id: PEC
structure: CCCCCSSC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
PF5:
id: PF5
name: 2,3,4,5,6-pentafluoro-l-phenylalanine
synonyms:
- F
- 2,3,4,5,6-pentafluoro-L-phenylalanine
- (2S)-2-amino-3-(2,3,4,5,6-pentafluorophenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: PF5
structure: '[NH3+][C@H](C(=O)[O-])Cc1c(F)c(F)c(c(c1F)F)F'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
PFF:
id: PFF
name: 4-fluoro-l-phenylalanine
synonyms:
- F
- (2S)-2-amino-3-(4-fluorophenyl)propanoic acid
- 4-fluoro-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: PFF
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)F'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
PFX:
id: PFX
name: (2s)-1-({2-[2-(carboxymethoxy)ethoxy]ethyl}amino)-1-oxo-3-(4-phosphonophenyl)propan-2-aminium
synonyms:
- (2S)-1-({2-[2-(carboxymethoxy)ethoxy]ethyl}amino)-1-oxo-3-(4-phosphonophenyl)propan-2-aminium
- '[(2S)-1-[2-[2-(carboxymethyloxy)ethoxy]ethylamino]-1-oxo-3-(4-phosphonophenyl)propan-2-yl]azanium'
- X
identifiers:
- ns: pdb-ccd
id: PFX
structure: '[O-]C(=O)COCCOCCNC(=O)[C@H](Cc1ccc(cc1)P(=O)([O-])[O-])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
PG1:
id: PG1
name: penicillin g acyl-serine
synonyms:
- S
- (2R,4S)-2-[(1R)-2-[(2S)-2-amino-3-oxido-3-oxo-propoxy]-2-oxo-1-(2-phenylethanoylamino)ethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylate
- (2R,4S)-2-{(1R)-2-[(2S)-2-amino-2-carboxylatoethoxy]-2-oxo-1-[(phenylacetyl)amino]ethyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylate
identifiers:
- ns: pdb-ccd
id: PG1
structure: O=C(N[C@@H]([C@@H]1[NH2+][C@H](C(S1)(C)C)C(=O)[O-])C(=O)OC[C@@H](C(=O)[O-])[NH3+])Cc1ccccc1
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
PH6:
id: PH6
name: (4s)-4-cyclohexyl-l-proline
synonyms:
- P
- (2S,4S)-4-cyclohexylpyrrolidine-2-carboxylic acid
- (4S)-4-cyclohexyl-L-proline
identifiers:
- ns: pdb-ccd
id: PH6
structure: '[O-]C(=O)[C@H]1[NH2+]C[C@@H](C1)C1CCCCC1'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
PH8:
id: PH8
name: 5-phenyl-l-norvaline
synonyms:
- 5-phenyl-L-norvaline
- (2S)-2-azanyl-5-phenyl-pentanoic acid
identifiers:
- ns: pdb-ccd
id: PH8
structure: '[O-]C(=O)[C@H](CCCc1ccccc1)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
PHA:
id: PHA
name: phenylalaninal
synonyms:
- F
- (2S)-2-amino-3-phenyl-propanal
- (2S)-2-amino-3-phenylpropanal
identifiers:
- ns: pdb-ccd
id: PHA
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccccc1'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
PHI:
id: PHI
name: iodo-phenylalanine
synonyms:
- F
- 4-iodo-L-phenylalanine
- (2S)-2-amino-3-(4-iodophenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: PHI
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)I'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
PHL:
id: PHL
name: l-phenylalaninol
synonyms:
- F
- (2S)-2-amino-3-phenylpropan-1-ol
- (2S)-2-amino-3-phenyl-propan-1-ol
identifiers:
- ns: pdb-ccd
id: PHL
structure: OC[C@H](Cc1ccccc1)[NH3+]
base_monomers:
- F
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
PIA:
id: PIA
name: '[(4z)-2-[(1s)-1-aminoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic
acid'
synonyms:
- AYG
- 2-[(4Z)-2-[(1S)-1-azanylethyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
- '[(4Z)-2-[(1S)-1-aminoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic
acid'
identifiers:
- ns: pdb-ccd
id: PIA
structure: C[C@@H](C1=N/C(=C\c2ccc(cc2)O)/C(=O)N1CC(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 19
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
r_displaced_atoms:
- molecule: Monomer
element: O
position: 21
charge: -1
PIV:
id: PIV
name: pivalic acid
synonyms:
- 2,2-dimethylpropanoic acid
- X
identifiers:
- ns: pdb-ccd
id: PIV
structure: '[O-]C(=O)C(C)(C)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
PLJ:
id: PLJ
name: methyl l-prolinate
synonyms:
- methyl (2S)-pyrrolidine-2-carboxylate
- methyl L-prolinate
identifiers:
- ns: pdb-ccd
id: PLJ
structure: COC(=O)[C@@H]1CCC[NH2+]1
base_monomers:
- P
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
PM3:
id: PM3
name: 2-amino-3-(4-phosphonomethyl-phenyl)-propionic acid
synonyms:
- F
- 4-(phosphonomethyl)-L-phenylalanine
- (2S)-2-amino-3-[4-(phosphonomethyl)phenyl]propanoic acid
identifiers:
- ns: pdb-ccd
id: PM3
structure: '[O-]C(=O)[C@H](Cc1ccc(cc1)CP(=O)(O)[O-])[NH3+]'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
PNZ:
id: PNZ
name: p-nitro-benzylamine
synonyms:
- (4-nitrophenyl)methanamine
- 1-(4-nitrophenyl)methanamine
identifiers:
- ns: pdb-ccd
id: PNZ
structure: '[NH3+]Cc1ccc(cc1)[N+](=O)[O-]'
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
POM:
id: POM
name: cis-5-methyl-4-oxoproline
synonyms:
- P
- (2S,5S)-5-methyl-4-oxo-pyrrolidine-2-carboxylic acid
- (5S)-5-methyl-4-oxo-L-proline
identifiers:
- ns: pdb-ccd
id: POM
structure: '[O-]C(=O)[C@@H]1CC(=O)[C@@H]([NH2+]1)C'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
PPN:
id: PPN
name: para-nitrophenylalanine
synonyms:
- F
- 4-nitro-L-phenylalanine
- (2S)-2-amino-3-(4-nitrophenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: PPN
structure: '[O-]C(=O)[C@H](Cc1ccc(cc1)[N+](=O)[O-])[NH3+]'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
PR3:
id: PR3
name: s,s-propylthiocysteine
synonyms:
- (2R)-2-amino-3-(propyldisulfanyl)propanal
- C
- (2R)-2-amino-3-propyldisulfanyl-propanal
identifiers:
- ns: pdb-ccd
id: PR3
structure: '[O-]C(=O)[C@@H]([NH3+])CSSCCC'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
PR4:
id: PR4
name: 1-[(2r)-2-carboxy-2-hydroxyethyl]-l-proline
synonyms:
- (1S,2S)-1-[(2R)-2,3-dihydroxy-3-oxo-propyl]pyrrolidine-2-carboxylic acid
- 1-[(2R)-2-carboxy-2-hydroxyethyl]-L-proline
identifiers:
- ns: pdb-ccd
id: PR4
structure: O[C@@H](C(=O)[O-])C[NH+]1CCC[C@H]1C(=O)[O-]
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
charge: -1
PR7:
id: PR7
name: 1-[(2s)-2-carboxy-2-hydroxyethyl]-l-proline
synonyms:
- (1S,2S)-1-[(2S)-2,3-dihydroxy-3-oxo-propyl]pyrrolidine-2-carboxylic acid
- 1-[(2S)-2-carboxy-2-hydroxyethyl]-L-proline
identifiers:
- ns: pdb-ccd
id: PR7
structure: O[C@H](C(=O)[O-])C[NH+]1CCC[C@H]1C(=O)[O-]
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
charge: -1
PRJ:
id: PRJ
name: (2s,3as,6r,7as)-6-hydroxyoctahydro-1h-indole-2-carboxylic acid
synonyms:
- (2S,3aS,6R,7aS)-6-hydroxy-2,3,3a,4,5,6,7,7a-octahydro-1H-indole-2-carboxylic
acid
- (2S,3aS,6R,7aS)-6-hydroxyoctahydro-1H-indole-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: PRJ
structure: O[C@@H]1CC[C@@H]2[C@H](C1)[NH2+][C@@H](C2)C(=O)[O-]
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
PRR:
id: PRR
name: 3-(methyl-pyridinium)alanine
synonyms:
- (2S)-2-azanyl-3-(1-methylpyridin-1-ium-3-yl)propanoic acid
- 3-(1-methylpyridinium-3-yl)-L-alanine
identifiers:
- ns: pdb-ccd
id: PRR
structure: '[O-]C(=O)[C@H](Cc1ccc[n+](c1)C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
PRS:
id: PRS
name: thioproline
synonyms:
- P
- (4R)-1,3-thiazolidine-4-carboxylic acid
identifiers:
- ns: pdb-ccd
id: PRS
structure: '[O-]C(=O)[C@@H]1CSC[NH2+]1'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
PRV:
id: PRV
name: (2r)-amino(2-nitrophenyl)ethanoic acid
synonyms:
- G
- (2R)-2-amino-2-(2-nitrophenyl)ethanoic acid
- (2R)-amino(2-nitrophenyl)ethanoic acid
identifiers:
- ns: pdb-ccd
id: PRV
structure: '[O-]C(=O)[C@@H](c1ccccc1[N+](=O)[O-])[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
PSH:
id: PSH
name: 1-thiophosphono-l-histidine
synonyms:
- (2S)-2-amino-3-[1-(hydroxy-sulfanyl-phosphoryl)imidazol-4-yl]propanoic acid
- 1-thiophosphono-L-histidine
- H
identifiers:
- ns: pdb-ccd
id: PSH
structure: '[O-]C(=O)[C@H](Cc1ncn(c1)P(=O)(S)[O-])[NH3+]'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
PSW:
id: PSW
name: 3-(sulfanylselanyl)-l-alanine
synonyms:
- U
- 3-(sulfanylselanyl)-L-alanine
- (2R)-2-amino-3-sulfanylselanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: PSW
structure: '[O-]C(=O)[C@@H]([NH3+])C[Se]S'
base_monomers:
- SEC
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
PTH:
id: PTH
name: ce1-methylene-hydroxy-phosphotyrosine
synonyms:
- 3-(hydroxymethyl)-O-phosphono-L-tyrosine
- Y
- (2S)-2-amino-3-[3-(hydroxymethyl)-4-phosphonooxy-phenyl]propanoic acid
identifiers:
- ns: pdb-ccd
id: PTH
structure: OCc1cc(ccc1OP(=O)([O-])[O-])C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
PTM:
id: PTM
name: alpha-methyl-o-phosphotyrosine
synonyms:
- (2S)-2-amino-2-methyl-3-(4-phosphonooxyphenyl)propanoic acid
- Y
- alpha-methyl-O-phosphono-L-tyrosine
identifiers:
- ns: pdb-ccd
id: PTM
structure: '[O-]C(=O)[C@](Cc1ccc(cc1)OP(=O)([O-])[O-])([NH3+])C'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
PVH:
id: PVH
name: histidine-methyl-ester
synonyms:
- H
- methyl (2S)-2-amino-3-(1H-imidazol-3-ium-4-yl)propanoate
- methyl 3-(1H-imidazol-3-ium-4-yl)-L-alaninate
identifiers:
- ns: pdb-ccd
id: PVH
structure: COC(=O)[C@H](Cc1c[nH]cn1)N
base_monomers:
- H
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
PVO:
id: PVO
name: 2,2-bis(oxidanyl)propanoic acid
synonyms:
- 2,2-bis(oxidanyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: PVO
structure: '[O-]C(=O)C(O)(O)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
PYA:
id: PYA
name: 3-(1,10-phenanthrol-2-yl)-l-alanine
synonyms:
- A
- 3-(1,10-phenanthrolin-2-yl)-L-alanine
- (2S)-2-amino-3-(1,10-phenanthrolin-2-yl)propanoic acid
identifiers:
- ns: pdb-ccd
id: PYA
structure: '[O-]C(=O)[C@H](Cc1ccc2c(n1)c1ncccc1cc2)[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
PYL:
id: PYL
name: pyrrolysine
synonyms:
- N~6~-{[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine
- (2S)-2-azanyl-6-[[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonylamino]hexanoic
acid
- O
identifiers:
- ns: pdb-ccd
id: PYL
structure: '[O-]C(=O)[C@H](CCCCNC(=O)[C@@H]1N=CC[C@H]1C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
PYX:
id: PYX
name: s-[s-thiopyridoxaminyl]cysteine
synonyms:
- 3-({[4-(aminomethyl)-5-hydroxy-6-methylpyridin-3-yl]methyl}disulfanyl)-L-alanine
- C
- (2R)-2-amino-3-[[4-(aminomethyl)-5-hydroxy-6-methyl-pyridin-3-yl]methyldisulfanyl]propanoic
acid
identifiers:
- ns: pdb-ccd
id: PYX
structure: '[NH3+]Cc1c(CSSC[C@@H](C(=O)[O-])[NH3+])cnc(c1O)C'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
QAC:
id: QAC
name: n-[4-(hydroxymethyl)benzoyl]-beta-alanine
synonyms:
- N-[4-(hydroxymethyl)benzoyl]-beta-alanine
- 3-[[4-(hydroxymethyl)phenyl]carbonylamino]propanoic acid
identifiers:
- ns: pdb-ccd
id: QAC
structure: OCc1ccc(cc1)C(=O)NCCC(=O)[O-]
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
QFG:
id: QFG
name: '{(4e)-2-[(1e)-4-amino-4-oxobutanimidoyl]-4-benzylidene-5-oxo-4,5-dihydro-1h-imidazol-1-yl}acetic
acid'
synonyms:
- 2-[(4E)-2-(4-azanyl-4-oxidanylidene-butanimidoyl)-5-oxidanylidene-4-(phenylmethylidene)imidazol-1-yl]ethanoic
acid
- '{(4E)-2-[(1E)-4-amino-4-oxobutanimidoyl]-4-benzylidene-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid'
- QFG
identifiers:
- ns: pdb-ccd
id: QFG
structure: '[O-]C(=O)CN1C(=N/C(=C/c2ccccc2)/C1=O)C(=N)CCC(=O)N'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
QIL:
id: QIL
name: n-formyl-l-isoleucine
synonyms:
- (2S,3S)-2-formamido-3-methyl-pentanoic acid
- N-formyl-L-isoleucine
identifiers:
- ns: pdb-ccd
id: QIL
structure: '[O-]C(=O)[C@H]([C@H](CC)C)NC=O'
base_monomers:
- I
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
QLG:
id: QLG
name: '[(4z)-2-[(1z)-4-amino-4-oxobutanimidoyl]-4-(2-methylpropylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic
acid'
synonyms:
- '[(4E)-2-[(1Z)-4-amino-4-oxobutanimidoyl]-4-(2-methylpropylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic
acid'
- 2-[2-(4-amino-4-oxo-butanimidoyl)-4-(2-methylpropylidene)-5-oxo-imidazol-1-yl]ethanoic
acid
- QLG
identifiers:
- ns: pdb-ccd
id: QLG
structure: '[O-]C(=O)CN1C(=NC(=CC(C)C)C1=O)C(=N)CCC(=O)N'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
QMM:
id: QMM
name: n,n-dimethyl-l-glutamine
synonyms:
- N,N-dimethyl-L-glutamine
- Q
- (2S)-2-azanyl-5-(dimethylamino)-5-oxo-pentanoic acid
identifiers:
- ns: pdb-ccd
id: QMM
structure: '[O-]C(=O)[C@H](CCC(=O)N(C)C)[NH3+]'
base_monomers:
- Q
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
QPH:
id: QPH
name: n-formyl-l-phenylalanine
synonyms:
- F
- (2S)-2-formamido-3-phenyl-propanoic acid
- N-formyl-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: QPH
structure: O=CN[C@H](C(=O)[O-])Cc1ccccc1
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 3
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 3
R1A:
id: R1A
name: 3-{[(2,2,5,5-tetramethyl-1-oxo-2,5-dihydro-1h-pyrrolium-3-yl)methyl]disulfanyl}-d-alanine
synonyms:
- 3-{[(2,2,5,5-tetramethyl-1-oxo-2,5-dihydro-1H-pyrrolium-3-yl)methyl]disulfanyl}-L-alanine
- (2R)-2-amino-3-[(2,2,5,5-tetramethyl-1-oxo-pyrrol-1-ium-3-yl)methyldisulfanyl]propanoic
acid
- C
identifiers:
- ns: pdb-ccd
id: R1A
structure: '[O-]C(=O)[C@H](CSSCC1=CC([N+](=O)C1(C)C)(C)C)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
R2T:
id: R2T
name: beta,gamma-dihydroxyglutamine
synonyms:
- (2S,3R,4S)-2,5-bis(azanyl)-3,4-bis(oxidanyl)-5-oxidanylidene-pentanoic acid
- (2S,3R,4S)-2,5-diamino-3,4-dihydroxy-5-oxopentanoic acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: R2T
structure: '[NH3+][C@@H]([C@H]([C@@H](C(=O)N)O)O)C(=O)[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 16
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 18
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
R4K:
id: R4K
name: (2s,3r)-2-azanyl-3-hydroxy-3-[(3s)-3-hydroxy-2-oxo-1h-indol-3-yl]propanoic
acid
synonyms:
- (3R)-3-[(3S)-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]-L-serine
- (2S,3R)-2-azanyl-3-oxidanyl-3-[(3S)-3-oxidanyl-2-oxidanylidene-1H-indol-3-yl]propanoic
acid
- W
identifiers:
- ns: pdb-ccd
id: R4K
structure: '[O-]C(=O)[C@H]([C@H]([C@]1(O)C(=O)Nc2c1cccc2)O)[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
RC7:
id: RC7
name: '{(2r)-4-(4-hydroxybenzyl)-2-[2-(1h-imidazol-4-yl)ethyl]-5-oxo-2,5-dihydro-1h-imidazol-1-yl}acetaldehyde'
synonyms:
- 2-[4-[(4-hydroxyphenyl)methyl]-2-[2-(1H-imidazol-4-yl)ethyl]-5-oxo-2H-imidazol-1-yl]ethanoic
acid
- HYG
- '{(2R)-4-(4-hydroxybenzyl)-2-[2-(1H-imidazol-4-yl)ethyl]-5-oxo-2,5-dihydro-1H-imidazol-1-yl}acetic
acid'
identifiers:
- ns: pdb-ccd
id: RC7
structure: '[O-]C(=O)CN1C(CCc2c[nH]cn2)N=C(C1=O)Cc1ccc(cc1)O'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
RE0:
id: RE0
name: 3-[(3r)-3-hydroxy-2-oxo-2,3-dihydro-1h-indol-3-yl]-l-alanine
synonyms:
- (2S)-2-azanyl-3-[(3R)-3-hydroxy-2-oxo-1H-indol-3-yl]propanoic acid
- 3-[(3R)-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]-L-alanine
- W
identifiers:
- ns: pdb-ccd
id: RE0
structure: '[O-]C(=O)[C@H](C[C@]1(O)C(=O)Nc2c1cccc2)[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
RE3:
id: RE3
name: 3-[(3s)-3-hydroxy-2-oxo-2,3-dihydro-1h-indol-3-yl]-l-alanine
synonyms:
- (2S)-2-azanyl-3-[(3S)-3-hydroxy-2-oxo-1H-indol-3-yl]propanoic acid
- 3-[(3S)-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]-L-alanine
- W
identifiers:
- ns: pdb-ccd
id: RE3
structure: '[O-]C(=O)[C@H](C[C@@]1(O)C(=O)Nc2c1cccc2)[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
RGL:
id: RGL
name: arginal
synonyms:
- amino{[(4S)-4-amino-5-oxopentyl]amino}methaniminium
- '[amino-[[(4S)-4-amino-5-oxo-pentyl]amino]methylidene]azanium'
- R
identifiers:
- ns: pdb-ccd
id: RGL
structure: '[O-]C(=O)[C@H](CCCNC(=[NH2+])N)[NH3+]'
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
RPI:
id: RPI
name: phospho-arginine
synonyms:
- (2~{S})-2-azanyl-5-[(~{N}-phosphonocarbamimidoyl)amino]pentanoic acid
- R
identifiers:
- ns: pdb-ccd
id: RPI
structure: '[O-]C(=O)[C@H](CCCNC(=[NH2+])NP(=O)([O-])[O-])[NH3+]'
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
RT0:
id: RT0
name: (2s,4s)-4-[4-(4-fluorophenyl)-1,2,3-triazol-1-yl]pyrrolidine-2-carboxylic
acid
synonyms:
- (2S,4S)-4-[4-(4-fluorophenyl)-1,2,3-triazol-1-yl]pyrrolidine-2-carboxylic acid
- (4S)-4-[4-(4-fluorophenyl)-1H-1,2,3-triazol-1-yl]-L-proline
identifiers:
- ns: pdb-ccd
id: RT0
structure: '[O-]C(=O)[C@H]1[NH2+]C[C@H](C1)n1nnc(c1)c1ccc(cc1)F'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
RVX:
id: RVX
name: o-[methyl(2-methylpropoxy)phosphoryl]-l-serine
synonyms:
- S
- O-[(R)-methyl(2-methylpropoxy)phosphoryl]-L-serine
- (2S)-2-azanyl-3-[methyl(2-methylpropoxy)phosphoryl]oxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: RVX
structure: '[NH3+][C@H](C(=O)[O-])CO[P@](=O)(OCC(C)C)C'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
RZ4:
id: RZ4
name: o-tert-butyl-l-serine
synonyms:
- S
- (2S)-2-azanyl-3-[(2-methylpropan-2-yl)oxy]propanoic acid
- O-tert-butyl-L-serine
identifiers:
- ns: pdb-ccd
id: RZ4
structure: '[NH3+][C@H](C(=O)[O-])COC(C)(C)C'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
S12:
id: S12
name: o-[(s)-hydroxy{[(2s)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-l-serine
synonyms:
- (2S)-2-azanyl-3-[[(2S)-3-octadec-9-enoyloxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-propanoic
acid
- O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine
identifiers:
- ns: pdb-ccd
id: S12
structure: CCCCCCCCC=CCCCCCCCC(=O)OC[C@@H](CO[P@](=O)(OC[C@@H](C(=O)[O-])[NH3+])[O-])O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 32
l_bond_atoms:
- molecule: Monomer
element: N
position: 35
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 34
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 35
- molecule: Monomer
element: H
position: 35
charge: 1
S1H:
id: S1H
name: 1-hexadecanosulfonyl-o-l-serine
synonyms:
- S
- O-(hexadecylsulfonyl)-L-serine
- (2S)-2-amino-3-hexadecylsulfonyloxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: S1H
structure: CCCCCCCCCCCCCCCCS(=O)(=O)OC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 24
l_bond_atoms:
- molecule: Monomer
element: N
position: 27
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 27
- molecule: Monomer
element: H
position: 27
charge: 1
S2C:
id: S2C
name: s-2-(boronoethyl)-l-cysteine
synonyms:
- (2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}ethyl)(trihydroxy)borate(1-)
- 2-[(2R)-2-azanyl-3-hydroxy-3-oxo-propyl]sulfanylethyl-trihydroxy-boranuide
- C
identifiers:
- ns: pdb-ccd
id: S2C
structure: '[O-]C(=O)[C@H](CSCC[B-](O)(O)O)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
S2P:
id: S2P
name: (2s)-2-amino-3-(4-hydroxy-1,2,5-thiadiazol-3-yl)propanoic acid
synonyms:
- A
- (2S)-2-amino-3-(4-hydroxy-1,2,5-thiadiazol-3-yl)propanoic acid
- 3-(4-hydroxy-1,2,5-thiadiazol-3-yl)-L-alanine
identifiers:
- ns: pdb-ccd
id: S2P
structure: '[O-]C(=O)[C@H](Cc1nsnc1[O-])[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
SAH:
id: SAH
name: s-adenosyl-l-homocysteine
synonyms:
- (2S)-2-amino-4-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methylsulfanyl]butanoic
acid
- C
- (2S)-2-amino-4-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic
acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: SAH
structure: '[O-]C(=O)[C@H](CCSC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 31
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 31
- molecule: Monomer
element: H
position: 31
charge: 1
SAO:
id: SAO
name: 5'-s-[(3s)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine
synonyms:
- '[(2~{S})-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]-1-oxidanyl-1-oxidanylidene-butan-2-yl]azanium'
- 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine
identifiers:
- ns: pdb-ccd
id: SAO
structure: '[O-]C(=O)[C@H](CCSC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 31
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 31
- molecule: Monomer
element: H
position: 31
charge: 1
SBL:
id: SBL
name: l-naphthyl-1-acetamido boronic acid alanine
synonyms:
- S
- '[(1R)-1-(acetylamino)-2-naphthalen-1-ylethyl](dihydroxy)(L-serinato-kappaO~3~)borate(1-)'
- '[(1R)-1-acetamido-2-naphthalen-1-yl-ethyl]-[(2S)-2-amino-3-hydroxy-3-oxo-propoxy]-dihydroxy-boron'
identifiers:
- ns: pdb-ccd
id: SBL
structure: CC(=O)N[C@H]([B-](OC[C@@H](C(=O)[O-])[NH3+])(O)O)Cc1cccc2c1cccc2
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
SCS:
id: SCS
name: 3-(ethyldisulfanyl)-l-alanine
synonyms:
- 3-(ethyldisulfanyl)-L-alanine
- C
- (2R)-2-amino-3-ethyldisulfanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: SCS
structure: '[O-]C(=O)[C@@H]([NH3+])CSSCC'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
SD2:
id: SD2
name: n-(sulfanylacetyl)tyrosylprolylmethioninamide
synonyms:
- N-(sulfanylacetyl)-L-tyrosyl-L-prolyl-L-methioninamide
- X
- (2S)-N-[(2S)-1-amino-4-methylsulfanyl-1-oxo-butan-2-yl]-1-[(2S)-3-(4-hydroxyphenyl)-2-(2-sulfanylethanoylamino)propanoyl]pyrrolidine-2-carboxamide
identifiers:
- ns: pdb-ccd
id: SD2
structure: CSCC[C@@H](C(=O)N)NC(=O)[C@@H]1CCCN1C(=O)[C@H](Cc1ccc(cc1)O)NC(=O)CS
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
SD4:
id: SD4
name: n-hydroxy-l-asparagine
synonyms:
- (2S)-2-azanyl-4-(oxidanylamino)-4-oxidanylidene-butanoic acid
identifiers:
- ns: pdb-ccd
id: SD4
structure: '[O-]C(=O)[C@@H]([NH3+])CC(=O)NO'
base_monomers:
- N
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
SDP:
id: SDP
name: 2-amino-3-(diethoxy-phosphoryloxy)-propionic acid
synonyms:
- S
- (2S)-2-amino-3-diethoxyphosphoryloxy-propanoic acid
- O-(diethoxyphosphoryl)-L-serine
identifiers:
- ns: pdb-ccd
id: SDP
structure: CCOP(=O)(OCC)OC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
SE7:
id: SE7
name: 2-amino-3-selenino-propionic acid
synonyms:
- U
- 3-selenino-L-alanine
- (2R)-2-azanyl-3-selenino-propanoic acid
identifiers:
- ns: pdb-ccd
id: SE7
structure: '[O-][Se](=O)C[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- SEC
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
SEB:
id: SEB
name: o-benzylsulfonyl-serine
synonyms:
- S
- (2S)-2-amino-3-(phenylmethylsulfonyloxy)propanoic acid
- O-(benzylsulfonyl)-L-serine
identifiers:
- ns: pdb-ccd
id: SEB
structure: '[NH3+][C@H](C(=O)[O-])COS(=O)(=O)Cc1ccccc1'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
SEC:
id: SEC
name: selenocysteine
synonyms:
- U
- 3-selanyl-L-alanine
- (2R)-2-azanyl-3-selanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: SEC
structure: '[O-]C(=O)[C@@H]([NH3+])C[SeH]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
base_monomers:
- C
SEE:
id: SEE
name: trihydroxy(l-serinato-kappao~3~)borate(1-)
synonyms:
- trihydroxy(L-serinato-kappaO~3~)borate(1-)
- '[(2S)-2-amino-3-hydroxy-3-oxo-propoxy]-trihydroxy-boron'
identifiers:
- ns: pdb-ccd
id: SEE
structure: O[B-](OC[C@@H](C(=O)[O-])[NH3+])(O)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
SEL:
id: SEL
name: 2-amino-1,3-propanediol
synonyms:
- S
- 2-aminopropane-1,3-diol
- 2-azanylpropane-1,3-diol
identifiers:
- ns: pdb-ccd
id: SEL
structure: OCC(CO)[NH3+]
base_monomers:
- S
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
SEM:
id: SEM
name: o-benzyl-l-serine
synonyms:
- S
- (2S)-2-azanyl-3-phenylmethoxy-propanoic acid
- O-benzyl-L-serine
identifiers:
- ns: pdb-ccd
id: SEM
structure: '[NH3+][C@H](C(=O)[O-])COCc1ccccc1'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
SEN:
id: SEN
name: o-[n,n-dimethylphosphoramidate]-l-serine
synonyms:
- S
- O-[(S)-(dimethylamino)(hydroxy)phosphoryl]-L-serine
- (2S)-2-amino-3-(dimethylamino-hydroxy-phosphoryl)oxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: SEN
structure: '[NH3+][C@H](C(=O)[O-])COP(=O)(N(C)C)[O-]'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
SGB:
id: SGB
name: o-[(s)-methyl(1-methylethoxy)phosphoryl]-l-serine
synonyms:
- S
- O-[(S)-methyl(1-methylethoxy)phosphoryl]-L-serine
- (2S)-2-amino-3-(methyl-propan-2-yloxy-phosphoryl)oxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: SGB
structure: '[NH3+][C@H](C(=O)[O-])CO[P@](=O)(OC(C)C)C'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
SHC:
id: SHC
name: s-hexylcysteine
synonyms:
- (2R)-2-amino-3-hexylsulfanyl-propanoic acid
- S-hexyl-L-cysteine
- C
identifiers:
- ns: pdb-ccd
id: SHC
structure: CCCCCCSC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
SHP:
id: SHP
name: (4-hydroxymaltosephenyl)glycine
synonyms:
- G
- (2S)-amino{4-[(2-O-alpha-D-mannopyranosyl-alpha-D-mannopyranosyl)oxy]phenyl}ethanoic
acid
- (2S)-2-amino-2-[4-[(2R,3S,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-oxan-2-yl]oxyphenyl]ethanoic
acid
identifiers:
- ns: pdb-ccd
id: SHP
structure: OC[C@H]1O[C@H](Oc2ccc(cc2)[C@@H](C(=O)[O-])[NH3+])[C@H]([C@H]([C@@H]1O)O)O[C@H]1O[C@H](CO)[C@H]([C@@H]([C@@H]1O)O)O
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
SHR:
id: SHR
name: n-(5-amino-5-carboxypentyl)glutamic acid
synonyms:
- (2S)-2-[[(5S)-5-amino-6-hydroxy-6-oxo-hexyl]amino]pentanedioic acid
- K
- N-[(5S)-5-amino-5-carboxypentyl]-L-glutamic acid
identifiers:
- ns: pdb-ccd
id: SHR
structure: '[O-]C(=O)CC[C@@H](C(=O)[O-])[NH2+]CCCC[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
SIB:
id: SIB
name: (2s)-2-amino-4-({[(2s,3s,4r,5r)-3,4-dihydroxy-5-(6-oxo-1,6-dihydro-9h-purin-9-yl)tetrahydrofuran-2-yl]methyl}thio)butanoic
acid
synonyms:
- (2S)-2-amino-4-[[(2S,3S,4R,5R)-3,4-dihydroxy-5-(6-oxo-1H-purin-9-yl)oxolan-2-yl]methylsulfanyl]butanoic
acid
- (2S)-2-amino-4-({[(2S,3S,4R,5R)-3,4-dihydroxy-5-(6-oxo-1,6-dihydro-9H-purin-9-yl)tetrahydrofuran-2-yl]methyl}sulfanyl)butanoic
acid (non-preferred name)
- C
identifiers:
- ns: pdb-ccd
id: SIB
structure: '[O-]C(=O)[C@H](CCSC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1nc[nH]c2=O)[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 32
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 32
- molecule: Monomer
element: H
position: 32
charge: 1
SKH:
id: SKH
name: (3~{s})-5-[[(5~{s})-5-azanyl-6-oxidanyl-6-oxidanylidene-hexyl]amino]-3-methyl-3-oxidanyl-5-oxidanylidene-pentanoic
acid
synonyms:
- (3~{S})-5-[[(5~{S})-5-azanyl-6-oxidanyl-6-oxidanylidene-hexyl]amino]-3-methyl-3-oxidanyl-5-oxidanylidene-pentanoic
acid
- K
identifiers:
- ns: pdb-ccd
id: SKH
structure: O=C(C[C@@](CC(=O)[O-])(O)C)NCCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
SLL:
id: SLL
name: (2s)-2-azanyl-6-[(4-hydroxy-4-oxo-butanoyl)amino]hexanoic acid
synonyms:
- (2S)-2-azanyl-6-[(4-hydroxy-4-oxo-butanoyl)amino]hexanoic acid
- N~6~-(3-carboxypropanoyl)-L-lysine
identifiers:
- ns: pdb-ccd
id: SLL
structure: O=C(CCC(=O)[O-])NCCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
SLZ:
id: SLZ
name: l-thialysine
synonyms:
- S-(2-aminoethyl)-L-cysteine
- (2R)-2-amino-3-(2-aminoethylsulfanyl)propanoic acid
- K
identifiers:
- ns: pdb-ccd
id: SLZ
structure: '[O-]C(=O)[C@@H]([NH3+])CSCC[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
SMF:
id: SMF
name: 4-sulfomethyl-l-phenylalanine
synonyms:
- F
- 4-(sulfomethyl)-L-phenylalanine
- (2S)-2-amino-3-[4-(sulfomethyl)phenyl]propanoic acid
identifiers:
- ns: pdb-ccd
id: SMF
structure: '[O-]C(=O)[C@H](Cc1ccc(cc1)CS(=O)(=O)[O-])[NH3+]'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
SOC:
id: SOC
name: dioxyselenocysteine
synonyms:
- 3-(dioxidoselanyl)-L-alanine
- U
identifiers:
- ns: pdb-ccd
id: SOC
structure: O=[Se-](=O)C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- SEC
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
SRZ:
id: SRZ
name: propoxy-l-serine
synonyms:
- S
- O-(3-hydroxypropyl)-L-serine
- (2S)-2-azanyl-3-(3-oxidanylpropoxy)propanoic acid
identifiers:
- ns: pdb-ccd
id: SRZ
structure: OCCCOC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
SUB:
id: SUB
name: 3-phenyl-2-{[4-(toluene-4-sulfonyl)-thiomorpholine-3-carbonyl]-amino}-propionic
acid ethyl ester
synonyms:
- ethyl 2-[[(3R,4R)-4-(4-methylphenyl)sulfonylthiomorpholin-3-yl]carbonylamino]-3-phenyl-propanoate
- X
- ethyl N-({(3R)-4-[(4-methylphenyl)sulfonyl]thiomorpholin-3-yl}carbonyl)-L-phenylalaninate
identifiers:
- ns: pdb-ccd
id: SUB
structure: CCOC(=O)C(Cc1ccccc1)NC(=O)[C@@H]1CSCCN1S(=O)(=O)c1ccc(cc1)C
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
SUI:
id: SUI
name: (3-amino-2,5-dioxo-1-pyrrolidinyl)acetic acid
synonyms:
- '[(3S)-3-amino-2,5-dioxopyrrolidin-1-yl]acetic acid'
- 2-[(3S)-3-amino-2,5-dioxo-pyrrolidin-1-yl]ethanoic acid
- DG
identifiers:
- ns: pdb-ccd
id: SUI
structure: '[O-]C(=O)CN1C(=O)C[C@@H](C1=O)N'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
SUN:
id: SUN
name: o-[(r)-(dimethylamino)(ethoxy)phosphoryl]-l-serine
synonyms:
- S
- O-[(R)-(dimethylamino)(ethoxy)phosphoryl]-L-serine
- (2S)-2-amino-3-(dimethylamino-ethoxy-phosphoryl)oxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: SUN
structure: CCO[P@](=O)(N(C)C)OC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
SVX:
id: SVX
name: o-[(r)-ethoxy(methyl)phosphoryl]-l-serine
synonyms:
- (2S)-2-azanyl-3-[ethoxy(methyl)phosphoryl]oxy-propanoic acid
- S
- O-[(R)-ethoxy(methyl)phosphoryl]-L-serine
identifiers:
- ns: pdb-ccd
id: SVX
structure: '[O-]C(=O)[C@@H]([NH3+])CO[P@](=O)(OCC)C'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
SVY:
id: SVY
name: o-[bis(1-methylethoxy)phosphoryl]-l-serine
synonyms:
- S
- O-[bis(propan-2-yloxy)phosphoryl]-L-serine
- (2S)-2-azanyl-3-di(propan-2-yloxy)phosphoryloxy-propanoic acid
identifiers:
- ns: pdb-ccd
id: SVY
structure: '[NH3+][C@H](C(=O)[O-])COP(=O)(OC(C)C)OC(C)C'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
SWG:
id: SWG
name: 2-[(4z)-2-[(1r)-1-amino-2-hydroxy-ethyl]-4-(1h-indol-3-ylmethylidene)-5-oxo-imidazol-1-yl]ethanoic
acid
synonyms:
- 2-[(4Z)-2-[(1R)-1-amino-2-hydroxy-ethyl]-4-(1H-indol-3-ylmethylidene)-5-oxo-imidazol-1-yl]ethanoic
acid
- SWG
identifiers:
- ns: pdb-ccd
id: SWG
structure: OC[C@@H](C1=N/C(=C\c2c[nH]c3c2cccc3)/C(=O)N1CC(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 23
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
SYS:
id: SYS
name: 3-[(2-amino-2-oxoethyl)selanyl]-l-alanine
synonyms:
- (2R)-2-amino-3-(2-amino-2-oxo-ethyl)selanyl-propanoic acid
- U
- 3-[(2-amino-2-oxoethyl)selanyl]-L-alanine
identifiers:
- ns: pdb-ccd
id: SYS
structure: NC(=O)C[Se]C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- SEC
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
T0I:
id: T0I
name: (2s)-2-amino-3-(2,4-dihydroxy-5-imidazol-1-yl-phenyl)propanoic acid
synonyms:
- (2S)-2-amino-3-(2,4-dihydroxy-5-imidazol-1-yl-phenyl)propanoic acid
- Y
identifiers:
- ns: pdb-ccd
id: T0I
structure: '[O-]C(=O)[C@H](Cc1cc(c(cc1O)O)n1cncc1)[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
T11:
id: T11
name: 4-[3-(trifluoromethyl)diaziridin-3-yl]-l-phenylalanine
synonyms:
- F
- (2S)-2-amino-3-[4-[3-(trifluoromethyl)-1,2-diaziridin-3-yl]phenyl]propanoic
acid
- 4-[3-(trifluoromethyl)diaziridin-3-yl]-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: T11
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)C1(NN1)C(F)(F)F'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
T66:
id: T66
name: 2-aminoethyllysine-carbonylmethylene-thymine
synonyms:
- (2R)-6-amino-2-[2-aminoethyl-[2-(5-methyl-2,4-dioxo-pyrimidin-1-yl)ethanoyl]amino]hexanoic
acid
- X
- N~2~-(2-aminoethyl)-N~2~-[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]-D-lysine
identifiers:
- ns: pdb-ccd
id: T66
structure: '[NH3+]CCN([C@@H](C(=O)[O-])CCCC[NH3+])C(=O)Cn1cc(C)c(=O)[nH]c1=O'
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
T8L:
id: T8L
name: thio-phosohothreonine
synonyms:
- (2~{S},3~{R})-2-azanyl-3-[oxidanyl(sulfanyl)phosphoryl]oxy-butanoic acid
- T
identifiers:
- ns: pdb-ccd
id: T8L
structure: '[O-]C(=O)[C@H]([C@H](OP(=O)(O)[S-])C)[NH3+]'
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
TA4:
id: TA4
name: (s)-2-[4-(aminomethyl)-1h-1,2,3-triazol-1-yl]-4-methylpentanoic acid
synonyms:
- (2S)-2-[4-(aminomethyl)-1,2,3-triazol-1-yl]-4-methyl-pentanoic acid
- (2S)-2-[4-(aminomethyl)-1H-1,2,3-triazol-1-yl]-4-methylpentanoic acid
- X
identifiers:
- ns: pdb-ccd
id: TA4
structure: '[NH3+]Cc1nnn(c1)[C@H](C(=O)[O-])CC(C)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
TAV:
id: TAV
name: n-methyl-n-{2-[(2-naphthylsulfonyl)amino]-5-[(2-naphthylsulfonyl)oxy]benzoyl}-l-aspartic
acid
synonyms:
- (2S)-2-[methyl-[2-(naphthalen-2-ylsulfonylamino)-5-naphthalen-2-ylsulfonyloxy-phenyl]carbonyl-amino]butanedioic
acid
- D
- N-methyl-N-({2-[(naphthalen-2-ylsulfonyl)amino]-5-[(naphthalen-2-ylsulfonyl)oxy]phenyl}carbonyl)-L-aspartic
acid
identifiers:
- ns: pdb-ccd
id: TAV
structure: '[O-]C(=O)C[C@H](N(C(=O)c1cc(ccc1[N-]S(=O)(=O)c1ccc2c(c1)cccc2)OS(=O)(=O)c1ccc2c(c1)cccc2)C)C(=O)[O-]'
base_monomers:
- D
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
TBG:
id: TBG
name: 3-methyl-l-valine
synonyms:
- V
- (2S)-2-azanyl-3,3-dimethyl-butanoic acid
- 3-methyl-L-valine
identifiers:
- ns: pdb-ccd
id: TBG
structure: '[NH3+][C@@H](C(C)(C)C)C(=O)[O-]'
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
TCQ:
id: TCQ
name: (1s,2r)-n-{(1e)-5-[(2s)-2-amino-2-carboxyethyl]-2-hydroxy-4-oxocyclohexa-2,5-dien-1-ylidene}-2-phenylcyclopropanaminium
synonyms:
- (1S,2R)-N-{(1E)-5-[(2S)-2-amino-2-carboxyethyl]-2-hydroxy-4-oxocyclohexa-2,5-dien-1-ylidene}-2-phenylcyclopropanaminium
- (E)-[5-[(2S)-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]-2-oxidanyl-4-oxidanylidene-cyclohexa-2,5-dien-1-ylidene]-[(1S,2R)-2-phenylcyclopropyl]azanium
- Y
identifiers:
- ns: pdb-ccd
id: TCQ
structure: '[NH3+][C@H](C(=O)[O-])CC1=C/C(=N\[C@H]2C[C@@H]2c2ccccc2)/C(=CC1=O)[O-]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
TCR:
id: TCR
name: cyclomethyltryptophan
synonyms:
- (3S)-2,3,4,9-tetrahydro-1H-beta-carboline-3-carboxylic acid
- (3S)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid
- W
identifiers:
- ns: pdb-ccd
id: TCR
structure: '[O-]C(=O)[C@H]1[NH2+]Cc2c(C1)c1ccccc1[nH]2'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
TEF:
id: TEF
name: 4-(2h-tetrazol-2-yl)-l-phenylalanine
synonyms:
- (2S)-2-azanyl-3-[4-(1,2,3,4-tetrazol-2-yl)phenyl]propanoic acid
- 4-(2H-tetrazol-2-yl)-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: TEF
structure: '[O-]C(=O)[C@H](Cc1ccc(cc1)n1nncn1)[NH3+]'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
TFQ:
id: TFQ
name: 4-(2,2,2-trifluoroethyl)-l-phenylalanine
synonyms:
- F
- 4-(2,2,2-trifluoroethyl)-L-phenylalanine
- (2S)-2-amino-3-[4-(2,2,2-trifluoroethyl)phenyl]propanoic acid
identifiers:
- ns: pdb-ccd
id: TFQ
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)CC(F)(F)F'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
TH6:
id: TH6
name: 4-hydroxy-l-threonine
synonyms:
- (2S,3S)-2-amino-3,4-dihydroxy-butanoic acid
- 4-hydroxy-L-threonine
- T
identifiers:
- ns: pdb-ccd
id: TH6
structure: OC[C@H]([C@@H](C(=O)[O-])[NH3+])O
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
THO:
id: THO
name: reduced threonine
synonyms:
- (2R,3R)-2-aminobutane-1,3-diol
- X
identifiers:
- ns: pdb-ccd
id: THO
structure: OC[C@H]([C@H](O)C)[NH3+]
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
THZ:
id: THZ
name: 1-[(4s)-4-amino-5-(1,3-benzothiazol-2-yl)-5-oxopentyl]guanidine
synonyms:
- 1-[(4S)-4-amino-5-(1,3-benzothiazol-2-yl)-5-oxopentyl]guanidine
- 1-[(4S)-4-azanyl-5-(1,3-benzothiazol-2-yl)-5-oxo-pentyl]guanidine
- R
identifiers:
- ns: pdb-ccd
id: THZ
structure: NC(=[NH2+])NCCC[C@@H](C(=O)c1nc2c(s1)cccc2)N
base_monomers:
- R
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
TIH:
id: TIH
name: beta(2-thienyl)alanine
synonyms:
- A
- 3-thiophen-2-yl-L-alanine
- (2S)-2-amino-3-thiophen-2-yl-propanoic acid
identifiers:
- ns: pdb-ccd
id: TIH
structure: '[O-]C(=O)[C@H](Cc1cccs1)[NH3+]'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
TIS:
id: TIS
name: o-(1,1-dihydroxyethyl)-l-serine
synonyms:
- O-(1,1-dihydroxyethyl)-L-serine
- (2S)-2-amino-3-(1,1-dihydroxyethoxy)propanoic acid
identifiers:
- ns: pdb-ccd
id: TIS
structure: '[NH3+][C@H](C(=O)[O-])COC(O)(O)C'
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
TLY:
id: TLY
name: (2s)-2-azanyl-6-(ethanethioylamino)hexanoic acid
synonyms:
- N~6~-ethanethioyl-L-lysine
- (2S)-2-azanyl-6-(ethanethioylamino)hexanoic acid
identifiers:
- ns: pdb-ccd
id: TLY
structure: CC(=S)NCCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
TMD:
id: TMD
name: (6,7-dihydro)4-[(e)-butenyl]-4,n-dimethyl-threonine
synonyms:
- (2S,3R,4R)-3-hydroxy-4-methyl-2-methylamino-octanoic acid
- T
- 4-butyl-2,4,5-trideoxy-2-(methylamino)-L-xylonic acid
identifiers:
- ns: pdb-ccd
id: TMD
structure: CCCC[C@H]([C@H]([C@@H](C(=O)[O-])[NH2+]C)O)C
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
TNB:
id: TNB
name: s-(2,3,6-trinitrophenyl)cysteine
synonyms:
- S-(2,4,6-trinitrophenyl)-L-cysteine
- (2R)-2-amino-3-(2,4,6-trinitrophenyl)sulfanyl-propanoic acid
- C
identifiers:
- ns: pdb-ccd
id: TNB
structure: '[O-]C(=O)[C@H](CSc1c(cc(cc1[N+](=O)[O-])[N+](=O)[O-])[N+](=O)[O-])[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 23
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 23
- molecule: Monomer
element: H
position: 23
charge: 1
TNQ:
id: TNQ
name: 6-[(carboxymethyl)amino]-7-hydroxy-l-tryptophan
synonyms:
- (2~{S})-2-azanyl-3-[6-(2-hydroxy-2-oxoethylamino)-7-oxidanyl-1~{H}-indol-3-yl]propanoic
acid
- 6-[(carboxymethyl)amino]-7-hydroxy-L-tryptophan
identifiers:
- ns: pdb-ccd
id: TNQ
structure: '[O-]C(=O)CNc1ccc2c(c1O)[nH]cc2C[C@@H](C(=O)[O-])[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
TNR:
id: TNR
name: o-(2-acetamido-2-deoxy-alpha-d-galactopyranosyl)-l-serine
synonyms:
- (2S)-3-[(2S,3R,4R,5R,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2-amino-propanoic
acid
- S
- (2S)-3-{[(2S,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}-2-aminopropanoic
acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: TNR
structure: OC[C@H]1O[C@H](OC[C@@H](C(=O)[O-])[NH3+])[C@@H]([C@H]([C@H]1O)O)NC(=O)C
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
TOQ:
id: TOQ
name: 6,7-dihydroxy-l-tryptophan
synonyms:
- (2S)-2-azanyl-3-[6,7-bis(oxidanyl)-1H-indol-3-yl]propanoic acid
- 6,7-dihydroxy-L-tryptophan
- W
identifiers:
- ns: pdb-ccd
id: TOQ
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1c[nH]c2c1ccc(c2O)O'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
TOX:
id: TOX
name: 1-hydroperoxy-l-tryptophan
synonyms:
- 1-hydroperoxy-L-tryptophan
- (2S)-2-azanyl-3-[1-(dioxidanyl)indol-3-yl]propanoic acid
identifiers:
- ns: pdb-ccd
id: TOX
structure: OOn1cc(c2c1cccc2)C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
TPJ:
id: TPJ
name: (5r)-5-tert-butyl-l-proline
synonyms:
- (2S,5R)-5-tert-butylpyrrolidine-2-carboxylic acid
- (5R)-5-tert-butyl-L-proline
identifiers:
- ns: pdb-ccd
id: TPJ
structure: '[O-]C(=O)[C@@H]1CC[C@@H]([NH2+]1)C(C)(C)C'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
TPK:
id: TPK
name: (1r)-1-[(2s)-pyrrolidin-2-yl]ethane-1,2-diol
synonyms:
- (1R)-1-[(2S)-pyrrolidin-2-yl]ethane-1,2-diol
identifiers:
- ns: pdb-ccd
id: TPK
structure: OC[C@@H]([C@@H]1CCC[NH2+]1)O
base_monomers:
- P
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
TPL:
id: TPL
name: tryptophanol
synonyms:
- (2S)-2-amino-3-(1H-indol-3-yl)propan-1-ol
- W
identifiers:
- ns: pdb-ccd
id: TPL
structure: OC[C@H](Cc1c[nH]c2c1cccc2)[NH3+]
base_monomers:
- W
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
TQI:
id: TQI
name: n-{[4-chloro-3-(trifluoromethyl)phenyl]sulfonyl}-l-tryptophan
synonyms:
- (2S)-2-[[4-chloro-3-(trifluoromethyl)phenyl]sulfonylamino]-3-(1H-indol-3-yl)propanoic
acid
- W
identifiers:
- ns: pdb-ccd
id: TQI
structure: '[O-]C(=O)[C@@H](NS(=O)(=O)c1ccc(c(c1)C(F)(F)F)Cl)Cc1c[nH]c2c1cccc2'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
TQQ:
id: TQQ
name: (s)-2-amino-3-(6,7-dihydro-6-imino-7-oxo-1h-indol-3-yl)propanoic acid
synonyms:
- 3-[(6Z)-6-imino-7-oxo-6,7-dihydro-1H-indol-3-yl]-L-alanine
- (2S)-2-amino-3-(6-imino-7-oxo-1H-indol-3-yl)propanoic acid
- W
identifiers:
- ns: pdb-ccd
id: TQQ
structure: '[O-]C(=O)[C@H](Cc1c[nH]c2c1C=CC(=N)C2=O)[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 19
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 19
- molecule: Monomer
element: H
position: 19
charge: 1
TQZ:
id: TQZ
name: 2-amino-3-pentasulfanylpropan-1-ol
synonyms:
- 3-pentasulfanyl-L-alanine
- (2R)-2-azanyl-3-(pentasulfanyl)propanoic acid
- C
identifiers:
- ns: pdb-ccd
id: TQZ
structure: '[O-]C(=O)[C@@H]([NH3+])CSSSSS'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
TRF:
id: TRF
name: n1-formyl-tryptophan
synonyms:
- (2S)-2-amino-3-(1-methanoylindol-3-yl)propanoic acid
- 1-formyl-L-tryptophan
- W
identifiers:
- ns: pdb-ccd
id: TRF
structure: O=Cn1cc(c2c1cccc2)C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
TRN:
id: TRN
name: nz2-tryptophan
synonyms:
- (2S)-2-amino-3-(1H-pyrrolo[5,4-b]pyridin-3-yl)propanoic acid
- 3-(1H-pyrrolo[2,3-b]pyridin-3-yl)-L-alanine
- W
identifiers:
- ns: pdb-ccd
id: TRN
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1c[nH]c2c1cccn2'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
TRW:
id: TRW
name: trw3-(2-amino-3-hydroxy-propyl)-6-(n'-cyclohexyl-hydrazino)octahydro-indol-7-ol
synonyms:
- (2S)-2-amino-3-[7-hydroxy-6-(2-phenylhydrazinyl)-1H-indol-3-yl]propanal
- (2S)-2-amino-3-[7-hydroxy-6-(2-phenylhydrazino)-1H-indol-3-yl]propanal
- W
identifiers:
- ns: pdb-ccd
id: TRW
structure: '[NH3+][C@H](C(=O)[O-])Cc1c[nH]c2c1ccc(c2O)NNc1ccccc1'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
TRX:
id: TRX
name: 6-hydroxytryptophan
synonyms:
- (2S)-2-azanyl-3-(6-oxidanyl-1H-indol-3-yl)propanoic acid
- 6-hydroxy-L-tryptophan
- W
identifiers:
- ns: pdb-ccd
id: TRX
structure: '[O-]C(=O)[C@H](Cc1c[nH]c2c1ccc(c2)O)[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
TRY:
id: TRY
name: (2z)-2-amino-3-(1h-indol-3-yl)prop-2-enoic acid
synonyms:
- (2Z)-2-amino-3-(1H-indol-3-yl)prop-2-enoic acid
- (Z)-2-azanyl-3-(1H-indol-3-yl)prop-2-enoic acid
- W
identifiers:
- ns: pdb-ccd
id: TRY
structure: '[O-]C(=O)/C(=C/c1c[nH]c2c1cccc2)/[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
TST:
id: TST
name: 4-methyl-2-{[4-(toluene-4-sulfonyl)-thiomorpholine-3-carbonyl]-amino}-pentanoic
acid
synonyms:
- N-({(3R)-4-[(4-methylphenyl)sulfonyl]thiomorpholin-3-yl}carbonyl)-L-leucine
- X
- (2S)-4-methyl-2-[[(3R)-4-(4-methylphenyl)sulfonylthiomorpholin-3-yl]carbonylamino]pentanoic
acid
identifiers:
- ns: pdb-ccd
id: TST
structure: CC(C[C@@H](C(=O)[O-])NC(=O)[C@@H]1CSCCN1S(=O)(=O)c1ccc(cc1)C)C
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
TSY:
id: TSY
name: (2s)-2-amino-3-trisulfanylpropanoic acid
synonyms:
- (2R)-2-azanyl-3-(trisulfanyl)propanoic acid
- 3-trisulfanyl-L-alanine
- C
identifiers:
- ns: pdb-ccd
id: TSY
structure: '[O-]C(=O)[C@@H]([NH3+])CSSS'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
TTQ:
id: TTQ
name: 6-amino-7-hydroxy-l-tryptophan
synonyms:
- 6-amino-7-hydroxy-L-tryptophan
- (2S)-2-amino-3-(6-amino-7-hydroxy-1H-indol-3-yl)propanoic acid
- W
identifiers:
- ns: pdb-ccd
id: TTQ
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1c[nH]c2c1ccc(c2O)N'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
TTS:
id: TTS
name: 3-((3e)-4-hydroxy-3-{[2-(4-hydroxyphenyl)ethyl]imino}-6-oxocyclohexa-1,4-dien-1-yl)alanine
synonyms:
- (2S)-2-amino-3-[(3E)-4-hydroxy-3-[2-(4-hydroxyphenyl)ethylimino]-6-oxo-1-cyclohexa-1,4-dienyl]propanoic
acid
- 3-[(3E)-4-hydroxy-3-{[2-(4-hydroxyphenyl)ethyl]imino}-6-oxocyclohexa-1,4-dien-1-yl]-L-alanine
- Y
identifiers:
- ns: pdb-ccd
id: TTS
structure: '[NH3+][C@H](C(=O)[O-])CC1=C/C(=N\CCc2ccc(cc2)O)/C(=CC1=O)[O-]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
TXY:
id: TXY
name: 3-[(5s)-4,5-dihydroxycyclohexa-1,3-dien-1-yl]-l-alanine
synonyms:
- 3-[(5S)-4,5-dihydroxycyclohexa-1,3-dien-1-yl]-L-alanine
- (2S)-2-azanyl-3-[(5S)-4,5-bis(oxidanyl)cyclohexa-1,3-dien-1-yl]propanoic acid
- Y
identifiers:
- ns: pdb-ccd
id: TXY
structure: '[O-]C(=O)[C@@H]([NH3+])CC1=CC=C([C@H](C1)O)O'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
TY1:
id: TY1
name: o-tert-butyl-l-tyrosine
synonyms:
- (2S)-2-azanyl-3-[4-[(2-methylpropan-2-yl)oxy]phenyl]propanoic acid
- Y
- O-tert-butyl-L-tyrosine
identifiers:
- ns: pdb-ccd
id: TY1
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)OC(C)(C)C'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
TY5:
id: TY5
name: o-benzyl-l-tyrosine
synonyms:
- O-benzyl-L-tyrosine
- Y
- (2S)-2-azanyl-3-(4-phenylmethoxyphenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: TY5
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)OCc1ccccc1'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
TY8:
id: TY8
name: 2,4-bis(hydroperoxy)-5-hydroxy-l-phenylalanine
synonyms:
- 2,4-bis(hydroperoxy)-5-hydroxy-L-phenylalanine
- (2S)-2-azanyl-3-(2,4-dihydroperoxy-5-hydroxy-phenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: TY8
structure: OOc1cc(OO)c(cc1C[C@@H](C(=O)[O-])[NH3+])O
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
TY9:
id: TY9
name: 3,4-bis(hydroperoxy)-5-hydroxy-l-phenylalanine
synonyms:
- 3,4-bis(hydroperoxy)-5-hydroxy-L-phenylalanine
- (2S)-2-azanyl-3-(3,4-dihydroperoxy-5-hydroxy-phenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: TY9
structure: OOc1c(O)cc(cc1OO)C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
TYB:
id: TYB
name: tyrosinal
synonyms:
- Y
- (2S)-2-amino-3-(4-hydroxyphenyl)propanal
identifiers:
- ns: pdb-ccd
id: TYB
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)O'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
TYE:
id: TYE
name: 4-[(2s)-2-amino-3-hydroxypropyl]phenol
synonyms:
- 4-[(2S)-2-amino-3-hydroxypropyl]phenol
- 4-[(2S)-2-azanyl-3-hydroxy-propyl]phenol
identifiers:
- ns: pdb-ccd
id: TYE
structure: OC[C@H](Cc1ccc(cc1)O)[NH3+]
base_monomers:
- Y
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
TYJ:
id: TYJ
name: 2,5-dihydroxy-n-methyl-l-tyrosine
synonyms:
- 2,5-dihydroxy-N-methyl-L-tyrosine
- Y
- (2S)-2-(methylamino)-3-(2,4,5-trihydroxyphenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: TYJ
structure: '[O-]C(=O)[C@@H]([NH2+]C)Cc1cc(O)c(cc1O)O'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
TYN:
id: TYN
name: aminobenzofurazan-o-tyrosine
synonyms:
- (2S)-2-amino-3-[4-[(7-amino-1,3-dihydro-2,1,3-benzoxadiazol-4-yl)oxy]phenyl]propanoic
acid
- Y
- O-(7-amino-1,3-dihydro-2,1,3-benzoxadiazol-4-yl)-L-tyrosine
identifiers:
- ns: pdb-ccd
id: TYN
structure: '[O-]C(=O)[C@H](Cc1ccc(cc1)Oc1ccc(c2c1NON2)N)[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 24
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 24
- molecule: Monomer
element: H
position: 24
charge: 1
TYO:
id: TYO
name: (4z,6e)-2-amino-7-hydroperoxy-4-[(e)-2-hydroxyvinyl]hepta-4,6-dienoic acid
synonyms:
- (2S,4Z,6E)-2-amino-7-hydroperoxy-4-[(E)-2-hydroxyethenyl]hepta-4,6-dienoic acid
- Y
- (2S,6E)-2-amino-7-hydroperoxy-4-(2-hydroxyethenyl)hepta-4,6-dienoic acid
identifiers:
- ns: pdb-ccd
id: TYO
structure: OC=CC(=C/C=C/OO)C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
TYQ:
id: TYQ
name: 3-amino-6-hydroxy-tyrosine
synonyms:
- 3-amino-6-hydroxy-L-tyrosine
- (2S)-2-amino-3-(5-amino-2,4-dihydroxy-phenyl)propanoic acid
- Y
identifiers:
- ns: pdb-ccd
id: TYQ
structure: '[O-]C(=O)[C@@H]([NH3+])Cc1cc(N)c(cc1O)O'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
TYT:
id: TYT
name: tyrosine derivative
synonyms:
- (2S)-2-amino-3-[(5E)-4-hydroxy-2-oxo-5-(2-phenylcyclopropyl)imino-1-cyclohex-3-enyl]propanoic
acid
- 3-{(5E)-4-hydroxy-2-oxo-5-[(2-phenylcyclopropyl)imino]cyclohex-3-en-1-yl}alanine
- Y
identifiers:
- ns: pdb-ccd
id: TYT
structure: '[O-]C(=O)[C@H](CC1C/C(=N\C2CC2c2ccccc2)/C(=CC1=O)[O-])[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 25
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 25
- molecule: Monomer
element: H
position: 25
charge: 1
TYX:
id: TYX
name: s-(2-anilino-2-oxoethyl)-l-cysteine
synonyms:
- S-[2-oxo-2-(phenylamino)ethyl]-L-cysteine
- (2R)-2-amino-3-(2-oxo-2-phenylazanyl-ethyl)sulfanyl-propanoic acid
- X
identifiers:
- ns: pdb-ccd
id: TYX
structure: '[NH3+][C@H](C(=O)[O-])CSCC(=O)Nc1ccccc1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
TYY:
id: TYY
name: 3-(4-hydroxy-3-imino-6-oxo-cyclohexa-1,4-dienyl)-alanine
synonyms:
- (2S)-2-amino-3-(4-hydroxy-3-imino-6-oxo-1-cyclohexa-1,4-dienyl)propanoic acid
- Y
- 3-[(3Z)-4-hydroxy-3-imino-6-oxocyclohexa-1,4-dien-1-yl]-L-alanine
identifiers:
- ns: pdb-ccd
id: TYY
structure: '[O-]C(=O)[C@H](CC1=CC(=[NH2+])C(=CC1=O)[O-])[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
TZB:
id: TZB
name: (4s)-2-[(1e)-1-aminoprop-1-enyl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid
synonyms:
- (4S)-2-[(1Z)-1-aminoprop-1-en-1-yl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid
- (4S)-2-[(Z)-1-aminoprop-1-enyl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid
- X
identifiers:
- ns: pdb-ccd
id: TZB
structure: '[O-]C(=O)[C@H]1CSC(=N1)/C(=C/C)/N'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
U2X:
id: U2X
name: o-(cyclohexylmethyl)-l-tyrosine
synonyms:
- (2S)-2-azanyl-3-[4-(cyclohexylmethoxy)phenyl]propanoic acid
- O-(cyclohexylmethyl)-L-tyrosine
identifiers:
- ns: pdb-ccd
id: U2X
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)OCC1CCCCC1'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
U3X:
id: U3X
name: 4-[(cyclohexylmethyl)amino]-l-phenylalanine
synonyms:
- 4-[(cyclohexylmethyl)amino]-L-phenylalanine
- (2S)-2-azanyl-3-[4-(cyclohexylmethylamino)phenyl]propanoic acid
identifiers:
- ns: pdb-ccd
id: U3X
structure: '[NH3+][C@H](C(=O)[O-])Cc1ccc(cc1)NCC1CCCCC1'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
UF0:
id: UF0
name: o-[(r)-hydroxy{[(3r)-3-hydroxy-4-{[3-({2-[(hydroxyacetyl)amino]ethyl}amino)-3-oxopropyl]amino}-2,2-dimethyl-4-oxobutyl]oxy}phosphoryl]-l-serine
synonyms:
- (2S)-2-azanyl-3-[hydroxy-[(3R)-3-hydroxy-4-[[3-[2-(2-hydroxyethanoylamino)ethylamino]-3-oxo-propyl]amino]-2,2-dimethyl-4-oxo-butoxy]phosphoryl]oxy-propanoic
acid
identifiers:
- ns: pdb-ccd
id: UF0
structure: OCC(=O)NCCNC(=O)CCNC(=O)[C@@H](C(COP(=O)(OC[C@@H](C(=O)[O-])[NH3+])[O-])(C)C)O
base_monomers:
- S
r_bond_atoms:
- molecule: Monomer
element: C
position: 27
l_bond_atoms:
- molecule: Monomer
element: N
position: 30
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 30
- molecule: Monomer
element: H
position: 30
charge: 1
UM2:
id: UM2
name: (2s)-2-amino-n-butyl-propanamide
synonyms:
- (2S)-2-amino-N-butyl-propanamide
- N-butyl-L-alaninamide
identifiers:
- ns: pdb-ccd
id: UM2
structure: CCCCNC(=O)[C@@H]([NH3+])C
base_monomers:
- A
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
l_displaced_atoms:
- molecule: Monomer
element: H
position: 5
UMA:
id: UMA
name: uridine-5'-diphosphate-n-acetylmuramoyl-l-alanine
synonyms:
- A
- (2S)-2-[[(2R)-2-[(2R,3R,4R,5S,6R)-3-acetamido-2-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-5-hydroxy-6-(hydroxymethyl)oxan-4-yl]oxypropanoyl]amino]propanoic
acid
- (2S)-2-{[(2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoyl]amino}propanoic
acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: UMA
structure: OC[C@H]1O[C@H](O[P@](=O)(O[P@@](=O)(OC[C@H]2O[C@H]([C@@H]([C@@H]2O)O)n2ccc(=O)[nH]c2=O)[O-])[O-])[C@@H]([C@H]([C@@H]1O)O[C@@H](C(=O)N[C@H](C(=O)[O-])C)C)NC(=O)C
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 53
l_bond_atoms:
- molecule: Monomer
element: N
position: 50
r_displaced_atoms:
- molecule: Monomer
element: O
position: 55
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 50
UN2:
id: UN2
name: 2-amino-4,4-dihydroxybutanoic acid
synonyms:
- (2S)-2-amino-4,4-dihydroxy-butanoic acid
- 4-hydroxy-L-homoserine
- X
identifiers:
- ns: pdb-ccd
id: UN2
structure: '[NH3+][C@H](C(=O)[O-])CC(O)O'
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
UNK:
id: UNK
name: unknown
synonyms:
- X
- (2S)-2-aminobutanoic acid
identifiers:
- ns: pdb-ccd
id: UNK
structure: '[O-]C(=O)[C@@H]([NH3+])CC'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
UOX:
id: UOX
name: 3-(oxido-lambda~4~-selanyl)-l-alanine
synonyms:
- U
- 3-(oxido-lambda~4~-selanyl)-L-alanine
- (2R)-2-azanyl-3-hydroseleninyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: UOX
structure: O=[Se-]C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- SEC
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
UU4:
id: UU4
name: (2s)-2-amino-4-(l-serylamino)butanoic acid
synonyms:
- (2S)-2-azanyl-4-[[(2S)-2-azanyl-3-oxidanyl-propanoyl]amino]butanoic acid
- (2S)-2-amino-4-(L-serylamino)butanoic acid
identifiers:
- ns: pdb-ccd
id: UU4
structure: OC[C@@H](C(=O)NCC[C@@H](C(=O)[O-])[NH3+])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
UU5:
id: UU5
name: (2s)-2-amino-4-[(oxoacetyl)amino]butanoic acid
synonyms:
- (2S)-2-azanyl-4-(oxaldehydoylamino)butanoic acid
- (2S)-2-amino-4-[(oxoacetyl)amino]butanoic acid
identifiers:
- ns: pdb-ccd
id: UU5
structure: O=CC(=O)NCC[C@@H](C(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
- molecule: Monomer
element: H
position: 13
charge: 1
VAD:
id: VAD
name: deaminohydroxyvaline
synonyms:
- V
- (2R)-2-hydroxy-3-methylbutanoic acid
- (2R)-2-hydroxy-3-methyl-butanoic acid
identifiers:
- ns: pdb-ccd
id: VAD
structure: O[C@@H](C(=O)[O-])C(C)C
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 6
charge: -1
VAH:
id: VAH
name: (3r)-3-hydroxy-l-norvaline
synonyms:
- (2S,3R)-2-azanyl-3-hydroxy-pentanoic acid
- (3R)-3-hydroxy-L-norvaline
identifiers:
- ns: pdb-ccd
id: VAH
structure: CC[C@H]([C@@H](C(=O)[O-])[NH3+])O
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
VB1:
id: VB1
name: n^6^-[(1r)-2-{[(1s)-1-carboxypropyl]amino}-2-oxo-1-(sulfanylmethyl)ethyl]-6-oxo-l-lysine
synonyms:
- (2S)-2-amino-6-[[(2R)-1-[[(2S)-1-hydroxy-1-oxo-butan-2-yl]amino]-1-oxo-3-sulfanyl-propan-2-yl]amino]-6-oxo-hexanoic
acid
- K
- N~6~-[(1R)-2-{[(1S)-1-carboxypropyl]amino}-2-oxo-1-(sulfanylmethyl)ethyl]-6-oxo-L-lysine
identifiers:
- ns: pdb-ccd
id: VB1
structure: SC[C@@H](C(=O)N[C@H](C(=O)[O-])CC)NC(=O)CCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 10
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 12
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 7
VH0:
id: VH0
name: (2s,4s)-4-[4-(aminomethyl)-1,2,3-triazol-1-yl]pyrrolidine-2-carboxylic acid
synonyms:
- (4S)-4-[4-(aminomethyl)-1H-1,2,3-triazol-1-yl]-L-proline
- (2S,4S)-4-[4-(aminomethyl)-1,2,3-triazol-1-yl]pyrrolidine-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: VH0
structure: '[NH3+]Cc1nnn(c1)[C@@H]1C[NH2+][C@@H](C1)C(=O)[O-]'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 20
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 22
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
VLL:
id: VLL
name: (2s)-2,3-diaminobutanoic acid
synonyms:
- (2S,3R)-2,3-diaminobutanoic acid
- X
- (2S,3R)-2,3-bis(azanyl)butanoic acid
identifiers:
- ns: pdb-ccd
id: VLL
structure: '[O-]C(=O)[C@H]([C@H]([NH3+])C)N'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 13
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 13
VMS:
id: VMS
name: 5'o-[n-(l-valyl)sulphamoyl]adenosine
synonyms:
- 5'-O-(L-valylsulfamoyl)adenosine
- X
- '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl N-[(2S)-2-amino-3-methyl-butanoyl]sulfamate'
identifiers:
- ns: pdb-ccd
id: VMS
structure: CC([C@@H](C(=O)[N-]S(=O)(=O)OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)N)C
l_bond_atoms:
- molecule: Monomer
element: N
position: 26
VOL:
id: VOL
name: l-valinol
synonyms:
- (2S)-2-amino-3-methylbutan-1-ol
- X
- (2S)-2-amino-3-methyl-butan-1-ol
identifiers:
- ns: pdb-ccd
id: VOL
structure: OC[C@H](C(C)C)[NH3+]
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
- molecule: Monomer
element: H
position: 8
charge: 1
VR0:
id: VR0
name: n~5~-[n-(methylcarbamoyl)carbamimidoyl]-l-ornithine
synonyms:
- N~5~-[N-(methylcarbamoyl)carbamimidoyl]-L-ornithine
- (2S)-2-azanyl-5-[[N-(methylcarbamoyl)carbamimidoyl]amino]pentanoic acid
identifiers:
- ns: pdb-ccd
id: VR0
structure: '[O-]C(=O)[C@@H]([NH3+])CCCNC(=[NH2+])NC(=O)NC'
base_monomers:
- R
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
VYA:
id: VYA
name: 2-[(4~{z})-2-[(1~{s})-1-azanyl-3-methyl-butyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
synonyms:
- 2-[(4~{Z})-2-[(1~{S})-1-azanyl-3-methyl-butyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
- LYG
identifiers:
- ns: pdb-ccd
id: VYA
structure: '[NH3+][C@H](C1=N/C(=C\c2ccc(cc2)O)/C(=O)N1CC(=O)[O-])CC(C)C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 22
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
WCR:
id: WCR
name: '[(2r,4z)-2-(aminomethyl)-2-hydroxy-4-(4-hydroxybenzylidene)-5-oxoimidazolidin-1-yl]acetic
acid'
synonyms:
- GYG
- 2-[(2R,4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-2-oxidanyl-5-oxidanylidene-imidazolidin-1-yl]ethanoic
acid
- '[(2R,4Z)-2-(aminomethyl)-2-hydroxy-4-(4-hydroxybenzylidene)-5-oxoimidazolidin-1-yl]acetic
acid'
identifiers:
- ns: pdb-ccd
id: WCR
structure: '[NH3+]C[C@@]1(O)N/C(=C\c2ccc(cc2)O)/C(=O)N1CC(=O)[O-]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 22
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
WFP:
id: WFP
name: 3,5-difluoro-l-phenylalanine
synonyms:
- (2S)-2-azanyl-3-(3,5-difluorophenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: WFP
structure: '[NH3+][C@H](C(=O)[O-])Cc1cc(F)cc(c1)F'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
WLU:
id: WLU
name: (4r)-5-hydroxy-n-methyl-l-leucine
synonyms:
- (2S,4R)-4-methyl-2-(methylamino)-5-oxidanyl-pentanoic acid
- (4R)-5-hydroxy-N-methyl-L-leucine
- L
identifiers:
- ns: pdb-ccd
id: WLU
structure: C[NH2+][C@H](C(=O)[O-])C[C@H](CO)C
base_monomers:
- L
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
WPA:
id: WPA
name: (betar)-beta-methoxy-l-phenylalanine
synonyms:
- F
- (2S,3R)-2-azanyl-3-methoxy-3-phenyl-propanoic acid
- (betaR)-beta-methoxy-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: WPA
structure: CO[C@@H]([C@@H](C(=O)[O-])[NH3+])c1ccccc1
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
WRP:
id: WRP
name: (betar)-beta-hydroxy-1-[(3r)-3-hydroxy-2-methylbutan-2-yl]-l-tryptophan
synonyms:
- (betaR)-beta-hydroxy-1-[(3R)-3-hydroxy-2-methylbutan-2-yl]-L-tryptophan
- (2S,3R)-2-azanyl-3-[1-[(3R)-2-methyl-3-oxidanyl-butan-2-yl]indol-3-yl]-3-oxidanyl-propanoic
acid
- W
identifiers:
- ns: pdb-ccd
id: WRP
structure: '[O-]C(=O)[C@H]([C@@H](c1cn(c2c1cccc2)C([C@H](O)C)(C)C)O)[NH3+]'
base_monomers:
- W
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 25
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 25
- molecule: Monomer
element: H
position: 25
charge: 1
WVL:
id: WVL
name: (2s,3r)-2-amino-3,5-dimethylhex-4-enoic acid
synonyms:
- V
- (2S,3R)-2-azanyl-3,5-dimethyl-hex-4-enoic acid
- (2S,3R)-2-amino-3,5-dimethylhex-4-enoic acid
identifiers:
- ns: pdb-ccd
id: WVL
structure: CC(=C[C@H]([C@@H](C(=O)[O-])[NH3+])C)C
base_monomers:
- V
r_bond_atoms:
- molecule: Monomer
element: C
position: 8
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
X2W:
id: X2W
name: n-acetyl-l-glutamyl 5-phosphate
synonyms:
- E
- N-acetyl-5-oxo-5-(phosphonooxy)-L-norvaline
- (2S)-2-acetamido-5-oxo-5-phosphonooxy-pentanoic acid
identifiers:
- ns: pdb-ccd
id: X2W
structure: CC(=O)N[C@H](C(=O)[O-])CCC(=O)OP(=O)([O-])[O-]
base_monomers:
- E
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
X9Q:
id: X9Q
name: '{(2s)-2-[(1s)-1-aminoethyl]-4-benzyl-5-oxo-2,5-dihydro-1h-imidazol-1-yl}acetic
acid'
synonyms:
- '{(2S)-2-[(1S)-1-aminoethyl]-4-benzyl-5-oxo-2,5-dihydro-1H-imidazol-1-yl}acetic
acid'
- 2-[2-[(1S)-1-aminoethyl]-5-oxo-4-(phenylmethyl)-2H-imidazol-1-yl]ethanoic acid
- AFG
identifiers:
- ns: pdb-ccd
id: X9Q
structure: C[C@@H](C1N=C(C(=O)N1CC(=O)[O-])Cc1ccccc1)[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 11
l_bond_atoms:
- molecule: Monomer
element: N
position: 5
r_displaced_atoms:
- molecule: Monomer
element: O
position: 13
charge: -1
XOK:
id: XOK
name: (2~{s})-2-azanyl-6-[[(6~{s})-6-sulfanyloctanoyl]amino]hexanoic acid
synonyms:
- (2~{S})-2-azanyl-6-[[(6~{S})-6-sulfanyloctanoyl]amino]hexanoic acid
identifiers:
- ns: pdb-ccd
id: XOK
structure: CC[C@@H](CCCCC(=O)NCCCC[C@@H](C(=O)[O-])[NH3+])S
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
XPL:
id: XPL
name: n~6~-[(3r,5r)-5-amino-3-methyl-d-prolyl]-l-lysine
synonyms:
- (2S)-2-azanyl-6-[[(2R,3R,5R)-5-azanyl-3-methyl-pyrrolidin-2-yl]carbonylamino]hexanoic
acid
- N~6~-[(3R,5R)-5-amino-3-methyl-D-prolyl]-L-lysine
- O
identifiers:
- ns: pdb-ccd
id: XPL
structure: '[O-]C(=O)[C@@H]([NH3+])CCCCNC(=O)[C@@H]1N[C@H](C[C@H]1C)[NH3+]'
base_monomers:
- PYL
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
XPR:
id: XPR
name: (2s,3as,6r,7as)-6-(sulfooxy)octahydro-1h-indole-2-carboxylic acid
synonyms:
- P
- (2S,3aS,6R,7aS)-6-sulfooxy-2,3,3a,4,5,6,7,7a-octahydro-1H-indole-2-carboxylic
acid
- (2S,3aS,6R,7aS)-6-(sulfooxy)octahydro-1H-indole-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: XPR
structure: '[O-]C(=O)[C@@H]1C[C@H]2[C@@H]([NH2+]1)C[C@@H](CC2)OS(=O)(=O)[O-]'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 11
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 11
- molecule: Monomer
element: H
position: 11
charge: 1
XW1:
id: XW1
name: (2s)-2-amino-7-ethoxy-7-oxoheptanoic acid
synonyms:
- (2S)-2-azanyl-7-ethoxy-7-oxidanylidene-heptanoic acid
- (2S)-2-amino-7-ethoxy-7-oxoheptanoic acid
identifiers:
- ns: pdb-ccd
id: XW1
structure: CCOC(=O)CCCC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 12
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
XX1:
id: XX1
name: n~6~-7h-purin-6-yl-l-lysine
synonyms:
- K
- N~6~-7H-purin-6-yl-L-lysine
- (2S)-2-amino-6-(7H-purin-6-ylamino)hexanoic acid
identifiers:
- ns: pdb-ccd
id: XX1
structure: '[O-]C(=O)[C@H](CCCCNc1ncnc2c1[nH]cn2)[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 21
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 21
- molecule: Monomer
element: H
position: 21
charge: 1
XXA:
id: XXA
name: 2,4,5-trideoxy-2-(methylamino)-4-[(2e)-penta-2,4-dien-1-yl]-l-xylonic acid
synonyms:
- (2S,3R,4R,6E)-3-hydroxy-4-methyl-2-(methylamino)nona-6,8-dienoic acid
- 2,4,5-trideoxy-2-(methylamino)-4-[(2E)-penta-2,4-dien-1-yl]-L-xylonic acid
identifiers:
- ns: pdb-ccd
id: XXA
structure: '[O-]C(=O)[C@@H]([NH2+]C)[C@@H]([C@@H](C/C=C/C=C)C)O'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
XXY:
id: XXY
name: 2-[(1r,2r)-1-amino-2-hydroxypropyl]-1-(carboxymethyl)-4-(1h-imidazol-5-ylmethyl)-1h-imidazol-5-olate
synonyms:
- 2-[(1R,2R)-1-amino-2-hydroxypropyl]-1-(carboxymethyl)-4-(1H-imidazol-5-ylmethyl)-1H-imidazol-5-olate
- 2-[(1R,2R)-1-amino-2-hydroxy-propyl]-3-(carboxymethyl)-5-(3H-imidazol-4-ylmethyl)imidazol-4-olate
- THG
identifiers:
- ns: pdb-ccd
id: XXY
structure: '[O-]C(=O)Cn1c(O)c(nc1[C@H]([C@H](O)C)[NH3+])Cc1cnc[nH]1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
XYC:
id: XYC
name: (2~{s})-2-azanyl-3-cyclopentyl-propanoic acid
synonyms:
- (2~{S})-2-azanyl-3-cyclopentyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: XYC
structure: '[NH3+][C@H](C(=O)[O-])CC1CCCC1'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
YCM:
id: YCM
name: s-(2-amino-2-oxoethyl)-l-cysteine
synonyms:
- S-(2-amino-2-oxoethyl)-L-cysteine
- (2R)-2-amino-3-(2-amino-2-oxo-ethyl)sulfanyl-propanoic acid
- C
identifiers:
- ns: pdb-ccd
id: YCM
structure: NC(=O)CSC[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 9
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
YCP:
id: YCP
name: (2s)-piperidine-2-carboxylic acid
synonyms:
- (2S)-piperidine-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: YCP
structure: '[O-]C(=O)[C@@H]1CCCC[NH2+]1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
YOF:
id: YOF
name: 3-fluorotyrosine
synonyms:
- 3-fluoro-L-tyrosine
- Y
- (2S)-2-amino-3-(3-fluoro-4-hydroxy-phenyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: YOF
structure: '[O-]C(=O)[C@H](Cc1ccc(c(c1)F)O)[NH3+]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
YPR:
id: YPR
name: (4r)-4-[(7-methoxy-2-phenylquinolin-4-yl)oxy]-l-proline
synonyms:
- (4R)-4-[(7-methoxy-2-phenylquinolin-4-yl)oxy]-L-proline
- (2S,4R)-4-(7-methoxy-2-phenyl-quinolin-4-yl)oxypyrrolidine-2-carboxylic acid
identifiers:
- ns: pdb-ccd
id: YPR
structure: COc1ccc2c(c1)nc(cc2O[C@H]1C[NH2+][C@@H](C1)C(=O)[O-])c1ccccc1
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 23
l_bond_atoms:
- molecule: Monomer
element: N
position: 17
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 17
- molecule: Monomer
element: H
position: 17
charge: 1
YPZ:
id: YPZ
name: 3-[(3z)-4-hydroxy-6-oxo-3-(2-phenylhydrazinylidene)cyclohexa-1,4-dien-1-yl]-l-alanine
synonyms:
- (2S)-2-azanyl-3-[(3Z)-4-oxidanyl-6-oxidanylidene-3-(phenylhydrazinylidene)cyclohexa-1,4-dien-1-yl]propanoic
acid
- 3-[(3Z)-4-hydroxy-6-oxo-3-(2-phenylhydrazinylidene)cyclohexa-1,4-dien-1-yl]-L-alanine
identifiers:
- ns: pdb-ccd
id: YPZ
structure: '[NH3+][C@H](C(=O)[O-])CC1=C/C(=N/Nc2ccccc2)/C(=CC1=O)[O-]'
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
YTH:
id: YTH
name: o-phosphono-l-allothreonine
synonyms:
- (2S,3S)-2-azanyl-3-phosphonooxy-butanoic acid
- O-phosphono-L-allothreonine
- T
identifiers:
- ns: pdb-ccd
id: YTH
structure: '[O-]C(=O)[C@H]([C@@H](OP(=O)([O-])[O-])C)[NH3+]'
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
YYA:
id: YYA
name: 2,4,5-trideoxy-2-(methylamino)-4-[(2z)-penta-2,4-dien-1-yl]-l-xylonic acid
synonyms:
- (2S,3R,4R,6Z)-3-hydroxy-4-methyl-2-(methylamino)nona-6,8-dienoic acid
- 2,4,5-trideoxy-2-(methylamino)-4-[(2Z)-penta-2,4-dien-1-yl]-L-xylonic acid
identifiers:
- ns: pdb-ccd
id: YYA
structure: '[O-]C(=O)[C@@H]([NH2+]C)[C@@H]([C@@H](C/C=C\C=C)C)O'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
Z01:
id: Z01
name: 3-[(2,2-dimethylpropanoyl)amino]-l-alanine
synonyms:
- A
- (2S)-2-azanyl-3-(2,2-dimethylpropanoylamino)propanoic acid
- 3-[(2,2-dimethylpropanoyl)amino]-L-alanine
identifiers:
- ns: pdb-ccd
id: Z01
structure: '[NH3+][C@H](C(=O)[O-])CNC(=O)C(C)(C)C'
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
Z3E:
id: Z3E
name: o-benzyl-l-threonine
synonyms:
- O-benzyl-L-threonine
- (2S,3R)-2-azanyl-3-phenylmethoxy-butanoic acid
identifiers:
- ns: pdb-ccd
id: Z3E
structure: C[C@H]([C@@H](C(=O)[O-])[NH3+])OCc1ccccc1
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
Z70:
id: Z70
name: (2s)-2-amino-4-(2-amino-1h-imidazol-5-yl)butanoic acid
synonyms:
- (2S)-2-amino-4-(2-amino-1H-imidazol-5-yl)butanoic acid
- (2S)-2-azanyl-4-(2-azanyl-1H-imidazol-5-yl)butanoic acid
identifiers:
- ns: pdb-ccd
id: Z70
structure: '[O-]C(=O)[C@@H]([NH3+])CCc1c[nH+]c([nH]1)N'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
ZBZ:
id: ZBZ
name: s-(phenylcarbonyl)-l-cysteine
synonyms:
- S-benzoyl-L-cysteine
- (2R)-2-azanyl-3-(phenylcarbonylsulfanyl)propanoic acid
identifiers:
- ns: pdb-ccd
id: ZBZ
structure: '[NH3+][C@H](C(=O)[O-])CSC(=O)c1ccccc1'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
ZCL:
id: ZCL
name: 3,4-dichloro-l-phenylalanine
synonyms:
- F
- (2S)-2-azanyl-3-(3,4-dichlorophenyl)propanoic acid
- 3,4-dichloro-L-phenylalanine
identifiers:
- ns: pdb-ccd
id: ZCL
structure: '[O-]C(=O)[C@H](Cc1ccc(c(c1)Cl)Cl)[NH3+]'
base_monomers:
- F
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
- molecule: Monomer
element: H
position: 15
charge: 1
ZFB:
id: ZFB
name: (3r)-3-{[(benzyloxy)carbonyl]amino}-2-oxo-4-phenylbutane-1-diazonium
synonyms:
- (3R)-2-oxo-4-phenyl-3-phenylmethoxycarbonylamino-butane-1-diazonium
- (3R)-3-{[(benzyloxy)carbonyl]amino}-2-oxo-4-phenylbutane-1-diazonium
- X
identifiers:
- ns: pdb-ccd
id: ZFB
structure: N#[N+]CC(=O)[C@@H](Cc1ccccc1)NC(=O)OCc1ccccc1
l_bond_atoms:
- molecule: Monomer
element: N
position: 15
l_displaced_atoms:
- molecule: Monomer
element: H
position: 15
ZU0:
id: ZU0
name: o-tert-butyl-l-threonine
synonyms:
- O-tert-butyl-L-threonine
- (2S,3R)-2-azanyl-3-[(2-methylpropan-2-yl)oxy]butanoic acid
- T
identifiers:
- ns: pdb-ccd
id: ZU0
structure: C[C@H]([C@@H](C(=O)[O-])[NH3+])OC(C)(C)C
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
ZYJ:
id: ZYJ
name: (4r)-4-({[(1e)-(3,4-dimethoxyphenyl)methylidene]amino}oxy)-l-proline
synonyms:
- (2S,4R)-4-[(E)-(3,4-dimethoxyphenyl)methylideneamino]oxypyrrolidine-2-carboxylic
acid
- (4R)-4-({[(E)-(3,4-dimethoxyphenyl)methylidene]amino}oxy)-L-proline
identifiers:
- ns: pdb-ccd
id: ZYJ
structure: COc1cc(/C=N/O[C@H]2C[NH2+][C@@H](C2)C(=O)[O-])ccc1OC
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 18
l_bond_atoms:
- molecule: Monomer
element: N
position: 12
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 12
- molecule: Monomer
element: H
position: 12
charge: 1
ZYK:
id: ZYK
name: (4r)-4-({[(3,4-dimethoxyphenyl)carbonyl]amino}oxy)-l-proline
synonyms:
- (2S,4R)-4-[(3,4-dimethoxyphenyl)carbonylamino]oxypyrrolidine-2-carboxylic acid
- (4R)-4-{[(3,4-dimethoxybenzoyl)amino]oxy}-L-proline
identifiers:
- ns: pdb-ccd
id: ZYK
structure: COc1cc(ccc1OC)C(=O)NO[C@H]1C[NH2+][C@@H](C1)C(=O)[O-]
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 24
l_bond_atoms:
- molecule: Monomer
element: N
position: 18
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 18
- molecule: Monomer
element: H
position: 18
charge: 1
ZZD:
id: ZZD
name: s-trityl-l-cysteine
synonyms:
- S-trityl-L-cysteine
- C
- (2R)-2-amino-3-tritylsulfanyl-propanoic acid
identifiers:
- ns: pdb-ccd
id: ZZD
structure: '[NH3+][C@H](C(=O)[O-])CSC(c1ccccc1)(c1ccccc1)c1ccccc1'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
ZZJ:
id: ZZJ
name: n^2^-methyl-l-alaninamide
synonyms:
- A
- N~2~-methyl-L-alaninamide
- (2S)-2-methylaminopropanamide
identifiers:
- ns: pdb-ccd
id: ZZJ
structure: C[C@H]([NH2+]C)C(=O)N
base_monomers:
- A
l_bond_atoms:
- molecule: Monomer
element: N
position: 4
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 4
- molecule: Monomer
element: H
position: 4
charge: 1
ZZU:
id: ZZU
name: (2s,3s)-3-hydroxyarginine
synonyms:
- (2S,3S)-2-amino-5-carbamimidamido-3-hydroxy-pentanoic acid
- (2S,3S)-2-amino-5-carbamimidamido-3-hydroxypentanoic acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: ZZU
structure: O[C@H]([C@@H](C(=O)[O-])[NH3+])CCNC(=[NH2+])N
r_bond_atoms:
- molecule: Monomer
element: C
position: 6
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 8
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 9
- molecule: Monomer
element: H
position: 9
charge: 1
T9E:
id: T9E
name: selenothreonine
synonyms:
- T
- (2~{R},3~{R})-2-azanyl-3-selanyl-butanoic acid
identifiers:
- ns: pdb-ccd
id: T9E
structure: '[O-]C(=O)[C@@H]([NH3+])[C@H]([SeH])C'
base_monomers:
- T
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
FOD:
id: FOD
name: (2s)-2-amino-4-[1-(trans-4-hydroxycyclohexyl)-1h-1,2,3-triazol-4-yl]butanoic
acid
synonyms:
- (2~{S})-2-azanyl-4-[1-(4-oxidanylcyclohexyl)-1,2,3-triazol-4-yl]butanoic acid
- (2S)-2-amino-4-[1-(trans-4-hydroxycyclohexyl)-1H-1,2,3-triazol-4-yl]butanoic
acid
identifiers:
- ns: pdb-ccd
id: FOD
structure: OC1CCC(CC1)n1nnc(c1)CC[C@@H](C(=O)[O-])[NH3+]
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
HOO:
id: HOO
name: (2~{s})-2-azanyl-3-[2,5-bis(oxidanylidene)imidazol-4-yl]propanoic acid
synonyms:
- (2~{S})-2-azanyl-3-[2,5-bis(oxidanylidene)imidazol-4-yl]propanoic acid
- H
identifiers:
- ns: pdb-ccd
id: HOO
structure: '[O-]C(=O)[C@H](CC1=NC(=O)[N-]C1=O)[NH3+]'
base_monomers:
- H
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 14
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 14
- molecule: Monomer
element: H
position: 14
charge: 1
F7Q:
id: F7Q
name: (2~{s})-2-azanyl-3-[1-(dioxidanyl)-4-oxidanylidene-cyclohexa-2,5-dien-1-yl]propanoic
acid
synonyms:
- (2~{S})-2-azanyl-3-[1-(dioxidanyl)-4-oxidanylidene-cyclohexa-2,5-dien-1-yl]propanoic
acid
- Y
identifiers:
- ns: pdb-ccd
id: F7Q
structure: OOC1(C=CC(=O)C=C1)C[C@@H](C(=O)[O-])[NH3+]
base_monomers:
- Y
r_bond_atoms:
- molecule: Monomer
element: C
position: 13
l_bond_atoms:
- molecule: Monomer
element: N
position: 16
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 16
- molecule: Monomer
element: H
position: 16
charge: 1
RF9:
id: RF9
name: n~6~-[(1r)-1-carboxyethyl]-l-lysine
synonyms:
- (2~{S})-2-azanyl-6-[[(2~{R})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]hexanoic
acid
- N~6~-[(1R)-1-carboxyethyl]-L-lysine
identifiers:
- ns: pdb-ccd
id: RF9
structure: '[O-]C(=O)[C@H](CCCC[NH2+][C@@H](C(=O)[O-])C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 15
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 17
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
JBY:
id: JBY
name: (2s)-2-{(4z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1h-imidazol-1-yl}propanoic
acid
synonyms:
- (2S)-2-{(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}propanoic
acid
- (2~{S})-2-[(4~{Z})-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]propanoic
acid
identifiers:
- ns: pdb-ccd
id: JBY
structure: '[NH3+]CC1=N/C(=C\c2ccc(cc2)O)/C(=O)N1[C@H](C(=O)[O-])C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 22
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
BJO:
id: BJO
name: (4z)-4-amino-4-{1-(carboxymethyl)-5-oxo-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1,5-dihydro-2h-imidazol-2-ylidene}butanoic
acid
synonyms:
- (4~{Z})-4-azanyl-4-[1-(2-hydroxy-2-oxoethyl)-5-oxidanylidene-4-[(4-oxidanylidenecyclohexa-2,5-dien-1-ylidene)methyl]imidazol-2-ylidene]butanoic
acid
- (4Z)-4-amino-4-{1-(carboxymethyl)-5-oxo-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1,5-dihydro-2H-imidazol-2-ylidene}butanoic
acid
identifiers:
- ns: pdb-ccd
id: BJO
structure: '[O-]C(=O)CN1C(=O)C(=N/C/1=C(\CCC(=O)[O-])/N)C=C1C=CC(=O)C=C1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 9
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
EOE:
id: EOE
name: beta3-proline
synonyms:
- 2-[(2~{S})-pyrrolidin-2-yl]ethanoic acid
identifiers:
- ns: pdb-ccd
id: EOE
structure: '[O-]C(=O)C[C@@H]1CCC[NH2+]1'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
FQA:
id: FQA
name: n~6~-benzyl-l-lysine
synonyms:
- N~6~-benzyl-L-lysine
- (2~{S})-2-azanyl-6-[(phenylmethyl)amino]hexanoic acid
identifiers:
- ns: pdb-ccd
id: FQA
structure: '[O-]C(=O)[C@H](CCCC[NH2+]Cc1ccccc1)[NH3+]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
9KP:
id: 9KP
name: (e)-n~6~-[(2e)-1-carboxy-3-(2-carboxyphenyl)prop-2-en-1-ylidene]-l-lysine
synonyms:
- 2-[(~{E},3~{E})-3-[(5~{S})-5-azanyl-6-oxidanyl-6-oxidanylidene-hexyl]imino-4-oxidanyl-4-oxidanylidene-but-1-enyl]benzoic
acid
- K
- (E)-N~6~-[(2E)-1-carboxy-3-(2-carboxyphenyl)prop-2-en-1-ylidene]-L-lysine
identifiers:
- ns: pdb-ccd
id: 9KP
structure: '[NH3+][C@H](C(=O)[O-])CCCC/[NH+]=C(/C(=O)[O-])\C=C\c1ccccc1C(=O)[O-]'
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 1
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 1
- molecule: Monomer
element: H
position: 1
charge: 1
GZJ:
id: GZJ
name: (2s)-2-(acetylamino)butanoic acid
synonyms:
- (2~{S})-2-acetamidobutanoic acid
- (2S)-2-(acetylamino)butanoic acid
identifiers:
- ns: pdb-ccd
id: GZJ
structure: CC[C@@H](C(=O)[O-])NC(=O)C
r_bond_atoms:
- molecule: Monomer
element: C
position: 5
l_bond_atoms:
- molecule: Monomer
element: N
position: 8
r_displaced_atoms:
- molecule: Monomer
element: O
position: 7
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 8
HJH:
id: HJH
name: (2~{s})-2-azanyl-3-(2-methyl-5-oxidanyl-1,2,3-triazol-4-yl)propanoic acid
synonyms:
- (2~{S})-2-azanyl-3-(2-methyl-5-oxidanyl-1,2,3-triazol-4-yl)propanoic acid
identifiers:
- ns: pdb-ccd
id: HJH
structure: '[O-]c1nn(nc1C[C@H]([NH3+])C(=O)[O-])C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 14
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 16
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
FHE:
id: FHE
name: 2-[(4~{z})-2-[(1~{r})-1-azanyl-2-oxidanylidene-propyl]-4-[[4-[(2-nitrophenyl)methoxy]phenyl]methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
synonyms:
- 2-[(4~{Z})-2-[(1~{R})-1-azanyl-2-oxidanylidene-propyl]-4-[[4-[(2-nitrophenyl)methoxy]phenyl]methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic
acid
- TYG
identifiers:
- ns: pdb-ccd
id: FHE
structure: '[O-]C(=O)CN1C(=N/C(=C\c2ccc(cc2)OCc2ccccc2[N+](=O)[O-])/C1=O)[C@H](C(=O)C)N'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 7
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
JLP:
id: JLP
name: (2s)-2-azanyl-6-[e-[5-(hydroxymethyl)-2-methyl-3-oxidanyl-pyridin-4-yl]methylideneamino]hexanoic
acid
synonyms:
- (2~{S})-2-azanyl-6-[(~{E})-[5-(hydroxymethyl)-2-methyl-3-oxidanyl-pyridin-4-yl]methylideneamino]hexanoic
acid
- K
identifiers:
- ns: pdb-ccd
id: JLP
structure: OCc1cnc(c(c1/C=N/CCCC[C@@H](C(=O)[O-])[NH3+])O)C
base_monomers:
- K
r_bond_atoms:
- molecule: Monomer
element: C
position: 17
l_bond_atoms:
- molecule: Monomer
element: N
position: 20
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 19
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 20
- molecule: Monomer
element: H
position: 20
charge: 1
JKH:
id: JKH
name: 4-amino-proline
synonyms:
- '[(3~{S},5~{S})-5-carboxypyrrolidin-3-yl]azanium'
- P
identifiers:
- ns: pdb-ccd
id: JKH
structure: '[O-]C(=O)[C@@H]1C[C@@H](C[NH2+]1)[NH3+]'
base_monomers:
- P
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 10
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 10
- molecule: Monomer
element: H
position: 10
charge: 1
F7P:
id: F7P
name: 1-[(3r)-3-hydroxy-2-methylbutan-2-yl]-l-tryptophan
synonyms:
- 1-[(3R)-3-hydroxy-2-methylbutan-2-yl]-L-tryptophan
- (2~{S})-2-azanyl-3-[1-[(3~{R})-2-methyl-3-oxidanyl-butan-2-yl]indol-3-yl]propanoic
acid
identifiers:
- ns: pdb-ccd
id: F7P
structure: '[O-]C(=O)[C@H](Cc1cn(c2c1cccc2)C([C@H](O)C)(C)C)[NH3+]'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 23
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 23
- molecule: Monomer
element: H
position: 23
charge: 1
F7S:
id: F7S
name: (4s)-5-hydroxy-n-methyl-l-leucine
synonyms:
- (2~{S},4~{S})-4-methyl-2-(methylamino)-5-oxidanyl-pentanoic acid
- (4S)-5-hydroxy-N-methyl-L-leucine
identifiers:
- ns: pdb-ccd
id: F7S
structure: C[NH2+][C@H](C(=O)[O-])C[C@@H](CO)C
r_bond_atoms:
- molecule: Monomer
element: C
position: 7
l_bond_atoms:
- molecule: Monomer
element: N
position: 2
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 2
- molecule: Monomer
element: H
position: 2
charge: 1
F7V:
id: F7V
name: (2s,4e)-2-aminohex-4-enoic acid
synonyms:
- (2S,4E)-2-aminohex-4-enoic acid
- (~{E},2~{S})-2-azanylhex-4-enoic acid
identifiers:
- ns: pdb-ccd
id: F7V
structure: '[O-]C(=O)[C@@H]([NH3+])C/C=C/C'
r_bond_atoms:
- molecule: Monomer
element: C
position: 2
l_bond_atoms:
- molecule: Monomer
element: N
position: 6
charge: -1
r_displaced_atoms:
- molecule: Monomer
element: O
position: 1
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 6
- molecule: Monomer
element: H
position: 6
charge: 1
SGergerOMeCys:
id: SGergerOMeCys
name: S-geranylgeranyl-L-cysteine methyl ester
identifiers:
- ns: mod
id: MOD:01119
structure: COC(=O)[C@H](CSC/C=C(/CC/C=C(/CC/C=C(/CCC=C(C)C)\C)\C)\C)[NH3+]
base_monomers:
- C
l_bond_atoms:
- molecule: Monomer
element: N
position: 29
charge: -1
l_displaced_atoms:
- molecule: Monomer
element: H
position: 29
- molecule: Monomer
element: H
position: 29
charge: 1