bpforms/alphabet/rna.yml
id: rna
name: RNA nucleotide monophosphates
description: The canonical RNA nucleotide monophosphates, plus non-canonical RNA nucleotide
monophosphates based on <a href="http://modomics.genesilico.pl/modifications">MODOMICS</a>
and the <a href="https://mods.rna.albany.edu/mods/">RNA Modification Database</a>
monomers:
01A:
id: 01A
name: 1,2′-O-dimethyladenosine
comments: <p>This compound is also listed under CA registry number 59867-24-2
as the monohydriodide salt, reflecting the form in which the first reported
synthesis was carried out.</p> <p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- 1,2'-O-dimethyladenosine
- m1Am
- œ
identifiers:
- ns: cas
id: 91101-00-7
- ns: rnamods
id: '97'
- ns: modomics.short_name
id: m1Am
- ns: modomics.new_nomenclature
id: 01A
structure: COC1C(O)C(OC1n1cnc2c1ncn(c2=N)C)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 22
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
01G:
id: 01G
name: 1,2′-O-dimethylguanosine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li></ul></p>
synonyms:
- 1,2'-O-dimethylguanosine
- m1Gm
- ε
identifiers:
- ns: modomics.new_nomenclature
id: 01G
- ns: cas
id: 73667-71-7
- ns: modomics.short_name
id: m1Gm
- ns: rnamods
id: '96'
structure: COC1C(O)C(OC1n1cnc2c1nc(N)n(c2=O)C)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
019A:
id: 019A
name: 1,2′-O-dimethylinosine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li></ul></p>
synonyms:
- m1Im
- ξ
- 1,2'-O-dimethylinosine
identifiers:
- ns: rnamods
id: '19'
- ns: cas
id: 65150-69-8
- ns: modomics.new_nomenclature
id: 019A
- ns: modomics.short_name
id: m1Im
structure: COC1C(O)C(OC1n1cnc2c1ncn(c2=O)C)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 22
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
1309U:
id: 1309U
name: 1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine
comments: <p></p> <p>Phylogenetic distribution<ul><li>eukarya rRNA</li></ul></p>
synonyms:
- α
- 1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine
- m1acp3Y
identifiers:
- ns: modomics.short_name
id: m1acp3Y
- ns: rnamods
id: '86'
- ns: cas
id: 52777-29-4
- ns: modomics.new_nomenclature
id: 1309U
structure: '[O-]C(=O)C(CCn1c(=O)c(cn(c1=O)C)C1OC(C(C1O)O)COP(=O)([O-])[O-])[NH3+]'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 22
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
1A:
id: 1A
name: 1-methyladenosine
comments: <p>First characterized as the base and later as the monoribonucleotide.</p>
<p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria tRNA</li><li>eukarya
tRNA</li><li>bacteria rRNA</li><li>eukarya rRNA</li></ul></p>
synonyms:
- A
- m1A
- '[(2R,3S,4R,5R)-5-(6-azanylidene-1-methyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
- '"'
- 6-hydro-1-methyladenosine-5'-monophosphate
- 1MA
- 1-methyladenosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 1MA
- ns: modomics.new_nomenclature
id: 1A
- ns: rnamods
id: '1'
- ns: modomics.short_name
id: m1A
- ns: cas
id: 15763-06-1
- ns: pubchem.compound
id: '27476'
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cnc2c1ncn(c2=N)C)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
1G:
id: 1G
name: 1-methylguanosine
comments: <p>Although the report in ref does not distinguish between the two subunits
in bacteria, contemporary knowledge shows that m1G is not in the bacterial SSU
(see SSU database) but is in the LSU (see table in Database section on rRNA
modification).</p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria
tRNA</li><li>eukarya tRNA</li><li>bacteria rRNA</li><li>eukarya rRNA</li></ul></p>
synonyms:
- '[(2R,3S,4R,5R)-5-(2-amino-1-methyl-6-oxo-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- G
- K
- m1G
- 1MG
- 1n-methylguanosine-5'-monophosphate
- 1-methylguanosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 1MG
- ns: cas
id: 2140-65-0
- ns: modomics.short_name
id: m1G
- ns: pubchem.compound
id: '96373'
- ns: modomics.new_nomenclature
id: 1G
- ns: rnamods
id: '29'
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cnc2c1nc(N)n(c2=O)C)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
19A:
id: 19A
name: 1-methylinosine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>eukarya
tRNA</li></ul></p>
synonyms:
- O
- m1I
identifiers:
- ns: pubchem.compound
id: '65095'
- ns: cas
id: 2140-73-0
- ns: modomics.new_nomenclature
id: 19A
- ns: rnamods
id: '18'
- ns: modomics.short_name
id: m1I
structure: OC1C(O)C(OC1n1cnc2c1ncn(c2=O)C)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 21
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
19U:
id: 19U
name: 1-methylpseudouridine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>eukarya
rRNA</li></ul></p>
synonyms:
- m1Y
- ']'
identifiers:
- ns: cas
id: 13860-38-3
- ns: rnamods
id: '55'
- ns: modomics.new_nomenclature
id: 19U
- ns: modomics.short_name
id: m1Y
structure: OC1C(O)C(OC1c1cn(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 20
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
28A:
id: 28A
name: 2,8-dimethyladenosine
synonyms:
- ±
identifiers:
- ns: modomics.new_nomenclature
id: 28A
- ns: modomics.short_name
id: m2,8A
structure: OC1C(O)C(OC1n1c(C)nc2c1nc(C)nc2N)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 22
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
msms2i6A:
id: msms2i6A
name: 2- methylthiomethylenethio-N6-isopentenyl-adenosine
synonyms:
- £
identifiers:
- ns: modomics.short_name
id: msms2i6A
structure: CSCSc1nc(NCC=C(C)C)c2c(n1)n(cn2)[C@@H]1O[C@@H](C(C1O)O)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 28
l_bond_atoms:
- molecule: Monomer
element: P
position: 31
r_displaced_atoms:
- molecule: Monomer
element: H
position: 28
l_displaced_atoms:
- molecule: Monomer
element: O
position: 34
charge: -1
21U:
id: 21U
name: 2-geranylthiouridine
synonyms:
- Γ
identifiers:
- ns: modomics.new_nomenclature
id: 21U
- ns: modomics.short_name
id: ges2U
structure: C/C(=C\CSc1nc(=O)ccn1[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-])/CCC=C(C)C
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 22
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
21C:
id: 21C
name: 2-lysidine
comments: <p>The registry number and Chemical Abstracts Index Name listed are
for the chloride salt. The registry number (144796-96-3) and Chemical Abstracts
Index Name (L-Lysine, N6-(1,4-dihydro-4-imino- 1-b-D-ribofuranosyl-2-pyrimidinyl)-)
assigned to the neutral nucleoside are less effective in retrieval of lysidine
literature. Alternate symbols are L and acp2C. The latter symbol is not recommended
because the notation acp has a different structural definition, and is more
commonly used in nucleoside acp3U. The common name "lysidine" was previously
assigned to 4,5-dihydro-2-methyl-1H-imidazole (registry number 534-26-9).</p>
<p>Phylogenetic distribution<ul><li>bacteria tRNA</li></ul></p>
synonyms:
- '}'
- k2C
- lysidine
identifiers:
- ns: cas
id: 116120-47-9
- ns: modomics.new_nomenclature
id: 21C
- ns: modomics.short_name
id: k2C
- ns: rnamods
id: '28'
structure: '[O-]C(=O)C(CCCCNC1[NH+]=C(N)C=CN1[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-])[NH3+]'
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 27
l_bond_atoms:
- molecule: Monomer
element: P
position: 30
r_displaced_atoms:
- molecule: Monomer
element: H
position: 27
l_displaced_atoms:
- molecule: Monomer
element: O
position: 33
charge: -1
2A:
id: 2A
name: 2-methyladenosine
comments: <p>Although ref reports m2A to be in a mixture of SSU and LSU subunits,
various more recent studies have shown that m2A is not present in the bacterial
SSU (see SSU database) but is in the LSU.</p> <p>Phylogenetic distribution<ul><li>archaea
tRNA</li><li>bacteria tRNA</li><li>bacteria rRNA</li></ul></p>
synonyms:
- m2A
- /
identifiers:
- ns: cas
id: 16526-56-0
- ns: modomics.short_name
id: m2A
- ns: modomics.new_nomenclature
id: 2A
- ns: rnamods
id: '2'
- ns: pubchem.compound
id: '261450'
structure: OC1C(O)C(OC1n1cnc2c1nc(C)nc2N)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 21
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
2164A:
id: 2164A
name: 2-methylthio cyclic N6-threonylcarbamoyladenosine
synonyms:
- ÿ
identifiers:
- ns: modomics.short_name
id: ms2ct6A
- ns: modomics.new_nomenclature
id: 2164A
structure: CSc1nc(C2C(=O)N[C@H](C2=O)[C@H](O)C)c2c(n1)n(cn2)[C@@H]1O[C@@H](C(C1O)O)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 32
l_bond_atoms:
- molecule: Monomer
element: P
position: 35
r_displaced_atoms:
- molecule: Monomer
element: H
position: 32
l_displaced_atoms:
- molecule: Monomer
element: O
position: 38
charge: -1
2160A:
id: 2160A
name: 2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine
comments: <p></p> <p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- ≠
- ms2io6A
identifiers:
- ns: cas
id: 52049-48-6
- ns: rnamods
id: '9'
- ns: modomics.short_name
id: ms2io6A
- ns: modomics.new_nomenclature
id: 2160A
structure: OC/C(=C/CNc1nc(SC)nc2c1ncn2[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-])/C
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 27
l_bond_atoms:
- molecule: Monomer
element: P
position: 30
r_displaced_atoms:
- molecule: Monomer
element: H
position: 27
l_displaced_atoms:
- molecule: Monomer
element: O
position: 33
charge: -1
2163A:
id: 2163A
name: 2-methylthio-N6-hydroxynorvalylcarbamoyladenosine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria
tRNA</li></ul></p>
synonyms:
- ms2hn6A
- 2-methylthio-N6-hydroxynorvalyl carbamoyladenosine
- ≈
identifiers:
- ns: modomics.short_name
id: ms2hn6A
- ns: cas
id: 146426-21-3
- ns: modomics.new_nomenclature
id: 2163A
- ns: rnamods
id: '15'
structure: CCC(C(C(=O)[O-])NC(=O)Nc1nc(SC)nc2c1ncn2[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-])O
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 32
l_bond_atoms:
- molecule: Monomer
element: P
position: 35
r_displaced_atoms:
- molecule: Monomer
element: H
position: 32
l_displaced_atoms:
- molecule: Monomer
element: O
position: 38
charge: -1
2161A:
id: 2161A
name: 2-methylthio-N6-isopentenyladenosine
comments: <p>Subsequently and independently characterized in E. coli tRNATyr.</p>
<p>Phylogenetic distribution<ul><li>bacteria tRNA</li></ul></p>
synonyms:
- ms2i6A
- '*'
identifiers:
- ns: rnamods
id: '7'
- ns: modomics.short_name
id: ms2i6A
- ns: pubchem.compound
id: '161337'
- ns: cas
id: 20859-00-1
- ns: modomics.new_nomenclature
id: 2161A
structure: CSc1nc(NCC=C(C)C)c2c(n1)n(cn2)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 27
l_bond_atoms:
- molecule: Monomer
element: P
position: 30
r_displaced_atoms:
- molecule: Monomer
element: H
position: 27
l_displaced_atoms:
- molecule: Monomer
element: O
position: 33
charge: -1
621A:
id: 621A
name: 2-methylthio-N6-methyladenosine
comments: '<p>Structure assigment is reported as a preliminary communication,
without details. Source of tRNA: Thermodesulfobacterium commune.</p> <p>Phylogenetic
distribution<ul><li>bacteria tRNA</li></ul></p>'
synonyms:
- ms2m6A
- ∞
identifiers:
- ns: modomics.new_nomenclature
id: 621A
- ns: modomics.short_name
id: ms2m6A
- ns: cas
id: 13406-51-4
- ns: rnamods
id: '5'
structure: CNc1nc(SC)nc2c1ncn2[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 23
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
r_displaced_atoms:
- molecule: Monomer
element: H
position: 23
l_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
2162A:
id: 2162A
name: 2-methylthio-N6-threonylcarbamoyladenosine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria
tRNA</li><li>eukarya tRNA</li></ul></p>
synonyms:
- A
- '['
- 12A
- 2-methylthio-N6-threonyl carbamoyladenosine
- ms2t6A
- (2S,3R)-2-[[9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-2-methylsulfanyl-purin-6-yl]carbamoylamino]-3-hydroxy-butanoic
acid
- (2S,3R)-2-({[9-{(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-2-(methylsulfanyl)-9H-purin-6-yl]carbamoyl}amino)-3-hydroxybutanoic
acid (non-preferred name)
- 2-methylthio-n6-(aminocarbonyl-l-threonyl)-adenosine-5'-monophosphate
identifiers:
- ns: modomics.short_name
id: ms2t6A
- ns: modomics.new_nomenclature
id: 2162A
- ns: rnamods
id: '12'
- ns: pdb-ccd
id: 12A
- ns: cas
id: 70333-82-3
structure: CSc1nc(NC(=O)N[C@@H](C(=O)O)[C@@H](O)C)c2c(n1)n(cn2)[C@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 35
l_bond_atoms:
- molecule: Monomer
element: P
position: 38
r_displaced_atoms:
- molecule: Monomer
element: H
position: 35
l_displaced_atoms:
- molecule: Monomer
element: O
position: 40
charge: -1
20U:
id: 20U
name: 2-selenouridine
synonyms:
- ω
identifiers:
- ns: modomics.short_name
id: se2U
- ns: modomics.new_nomenclature
id: 20U
structure: OC1C(O)C(OC1n1ccc(=O)[nH]c1=[Se])COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 19
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 22
charge: -1
02U:
id: 02U
name: 2-thio-2′-O-methyluridine
comments: <p>Preliminary communication of structural characterization and chemical
synthesis is given in.</p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li></ul></p>
synonyms:
- ∏
- 2-thio-2'-O-methyluridine
- s2Um
identifiers:
- ns: rnamods
id: '60'
- ns: modomics.new_nomenclature
id: 02U
- ns: modomics.short_name
id: s2Um
- ns: cas
id: 113886-72-9
structure: COC1C(O)C(OC1n1ccc(=O)[nH]c1=S)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 20
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
2C:
id: 2C
name: 2-thiocytidine
comments: <p>Initial structural and spectroscopic data are reported in, without
derivation of a final structure.</p> <p>Phylogenetic distribution<ul><li>archaea
tRNA</li><li>bacteria tRNA</li></ul></p>
synonyms:
- '%'
- '[(2R,3S,4R,5R)-5-(4-azanyl-2-sulfanylidene-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- RSP
- s2C
- 4-amino-1-(5-o-phosphono-beta-d-ribofuranosyl)pyrimidine-2(1h)-thione
identifiers:
- ns: cas
id: 13239-97-9
- ns: pdb-ccd
id: RSP
- ns: pubchem.compound
id: '3011746'
- ns: modomics.new_nomenclature
id: 2C
- ns: rnamods
id: '23'
- ns: modomics.short_name
id: s2C
structure: O[C@H]1[C@@H](O)[C@H](O[C@H]1n1ccc(nc1=S)N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 22
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
2U:
id: 2U
name: 2-thiouridine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria
tRNA</li><li>eukarya tRNA</li></ul></p>
synonyms:
- '2'
- s2U
identifiers:
- ns: cas
id: 20235-78-3
- ns: modomics.short_name
id: s2U
- ns: pubchem.compound
id: '3036443'
- ns: modomics.new_nomenclature
id: 2U
- ns: rnamods
id: '57'
structure: OC1C(O)C(OC1n1ccc(=O)[nH]c1=S)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 19
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 22
charge: -1
0A:
id: 0A
name: 2′-O-methyladenosine
comments: <p>Occurrence is rare in eukaryotes. First characterized as an O-2'
or O-3' methyl derivative, and subsequently shown to be O-2'.</p> <p>Phylogenetic
distribution<ul><li>archaea tRNA</li><li>bacteria tRNA</li><li>eukarya tRNA</li><li>archaea
rRNA</li><li>bacteria rRNA</li><li>eukarya rRNA</li><li>eukarya mRNA</li><li>eukarya
snRNA</li></ul></p>
synonyms:
- A
- Am
- 2'-o-methyladenosine 5'-(dihydrogen phosphate)
- 2'-O-methyladenosine 5'-(dihydrogen phosphate)
- A2M
- '[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-4-methoxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- 2'-O-methyladenosine
- ':'
identifiers:
- ns: pdb-ccd
id: A2M
- ns: modomics.new_nomenclature
id: 0A
- ns: modomics.short_name
id: Am
- ns: cas
id: 2140-79-6
- ns: rnamods
id: '4'
structure: CO[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cnc2c1ncnc2N)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 7
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 7
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
0C:
id: 0C
name: 2′-O-methylcytidine
comments: <p>Cm was first characterized as an O-2' or O-3' methyl derivative,
and subsequently shown to be O-2'.</p> <p>Phylogenetic distribution<ul><li>archaea
tRNA</li><li>bacteria tRNA</li><li>eukarya tRNA</li><li>archaea rRNA</li><li>bacteria
rRNA</li><li>eukarya rRNA</li><li>eukarya mRNA</li><li>eukarya snRNA</li></ul></p>
synonyms:
- o2'-methylycytidine-5'-monophosphate
- Cm
- OMC
- 2'-O-methylcytidine 5'-(dihydrogen phosphate)
- 2'-O-methylcytidine
- C
- B
- '[(2R,3R,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-4-methoxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: modomics.new_nomenclature
id: 0C
- ns: cas
id: 2140-72-9
- ns: pdb-ccd
id: OMC
- ns: modomics.short_name
id: Cm
- ns: pubchem.compound
id: '150971'
- ns: rnamods
id: '22'
structure: CO[C@H]1[C@H](O)[C@@H](O[C@H]1n1ccc(nc1=O)N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 7
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 7
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
0G:
id: 0G
name: 2′-O-methylguanosine
comments: <p>First characterized as an O-2' or O-3' methyl derivative, and subsequently
shown to be O-2'.</p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria
tRNA</li><li>eukarya tRNA</li><li>archaea rRNA</li><li>bacteria rRNA</li><li>eukarya
rRNA</li><li>eukarya mRNA</li><li>eukarya snRNA</li></ul></p>
synonyms:
- G
- o2'-methylguanosine-5'-monophosphate
- Gm
- 2'-O-methylguanosine
- 2'-O-methylguanosine 5'-(dihydrogen phosphate)
- '#'
- OMG
- '[(2R,3R,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxy-4-methoxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: OMG
- ns: modomics.short_name
id: Gm
- ns: rnamods
id: '32'
- ns: modomics.new_nomenclature
id: 0G
- ns: pubchem.compound
id: '188959'
- ns: cas
id: 2140-71-8
structure: CO[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cnc2c1nc(N)[nH]c2=O)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 7
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 7
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
09A:
id: 09A
name: 2′-O-methylinosine
comments: <p>More thorough characterization is reported in.</p> <p>Phylogenetic
distribution<ul><li>eukarya rRNA</li></ul></p>
synonyms:
- ≤
- 2'-O-methylinosine
- Im
identifiers:
- ns: modomics.short_name
id: Im
- ns: cas
id: 3881-21-8
- ns: modomics.new_nomenclature
id: 09A
- ns: rnamods
id: '81'
structure: COC1C(O)C(OC1n1cnc2c1nc[nH]c2=O)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 22
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
09U:
id: 09U
name: 2′-O-methylpseudouridine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>eukarya
tRNA</li><li>eukarya rRNA</li><li>eukarya snRNA</li></ul></p>
synonyms:
- Ym
- Z
- 2'-O-methylpseudouridine
identifiers:
- ns: modomics.short_name
id: Ym
- ns: modomics.new_nomenclature
id: 09U
- ns: rnamods
id: '56'
- ns: cas
id: 2140-68-3
structure: COC1C(O)C(OC1c1c[nH]c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 21
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
0U:
id: 0U
name: 2′-O-methyluridine
comments: <p>First characterized as an O-2' or O-3' methyl derivative, and subsequently
shown to be O-2'.</p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria
tRNA</li><li>eukarya tRNA</li><li>archaea rRNA</li><li>bacteria rRNA</li><li>eukarya
rRNA</li><li>eukarya mRNA</li><li>eukarya snRNA</li></ul></p>
synonyms:
- 2'-O-methyluridine
- '[(2R,3R,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-4-methoxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- U
- o2'-methyluridine 5'-monophosphate
- Um
- 2'-O-methyluridine 5'-(dihydrogen phosphate)
- J
- OMU
identifiers:
- ns: modomics.short_name
id: Um
- ns: modomics.new_nomenclature
id: 0U
- ns: cas
id: 2140-76-3
- ns: rnamods
id: '53'
- ns: pdb-ccd
id: OMU
structure: CO[C@H]1[C@H](O)[C@@H](O[C@H]1n1ccc(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 7
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 7
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
0503U:
id: 0503U
name: "2′-O-methyluridine 5-oxyacetic acid methyl ester\t"
synonyms:
- Ͽ
identifiers:
- ns: modomics.short_name
id: mcmo5Um
- ns: modomics.new_nomenclature
id: 0503U
structure: COC1[C@@H](O)[C@H](O[C@H]1n1cc(OCC(=O)OC)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 29
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 32
charge: -1
00A:
id: 00A
name: 2′-O-ribosyladenosine (phosphate)
comments: "<p>A nucleoside component of yeast tRNA was isolated and tentatively\
\ characterized as 2'(3')-O-ribosyladenosine by Hall, but whether the source\
\ material was tRNA was later concluded to be uncertain. Substitution at O-2'\
\ vs. O-3' was not established in an early reported synthesis. A recent and\
\ more detailed synthesis is given in. Ar registry number: 28269-89-8, Chemical\
\ Abstracts Index Name: Adenosine, 2'-O-b-D-ribofuranosyl-.</p> <p>Phylogenetic\
\ distribution<ul><li>eukarya tRNA</li></ul></p>"
synonyms:
- ^
- V3L
- 2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate)
- Ar(p)
- '[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- 2'-o-(5-o-phosphono-alpha-d-ribofuranosyl)adenosine 5'-(dihydrogen phosphate)
- 2'-O-ribosyladenosine (phosphate)
identifiers:
- ns: cas
id: 28050-13-7
- ns: pdb-ccd
id: V3L
- ns: modomics.new_nomenclature
id: 00A
- ns: rnamods
id: '16'
- ns: modomics.short_name
id: Ar(p)
structure: O[C@@H]1[C@@H](O[C@H]([C@@H]1O)COP(=O)(O)O)O[C@@H]1[C@H](O)[C@@H](O[C@@H]1n1cnc2c1ncnc2N)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 23
l_bond_atoms:
- molecule: Monomer
element: P
position: 41
r_displaced_atoms:
- molecule: Monomer
element: H
position: 23
l_displaced_atoms:
- molecule: Monomer
element: O
position: 43
charge: -1
00G:
id: 00G
name: 2′-O-ribosylguanosine (phosphate)
comments: "<p>This structure was initially reported in; more extensive structural\
\ data are presented in.\r\nGr registry number: 148711-49-3, Chemical Abstracts\
\ Index Name: Guanosine, 2'-O-b-D-ribofuranosyl-.</p> <p>Phylogenetic distribution<ul><li>eukarya\
\ tRNA</li></ul></p>"
synonyms:
- 2'-O-ribosylguanosine (phosphate)
- ℑ
- Gr(p)
identifiers:
- ns: modomics.short_name
id: Gr(p)
- ns: pubchem.compound
id: '131365'
- ns: rnamods
id: '36'
- ns: cas
id: 131293-20-4
- ns: modomics.new_nomenclature
id: 00G
structure: Nc1[nH]c(=O)c2c(n1)n(cn2)[C@@H]1O[C@@H](C([C@@H]1O[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-])O)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 38
l_bond_atoms:
- molecule: Monomer
element: P
position: 41
r_displaced_atoms:
- molecule: Monomer
element: H
position: 38
l_displaced_atoms:
- molecule: Monomer
element: O
position: 44
charge: -1
03U:
id: 03U
name: 3,2′-O-dimethyluridine
comments: <p></p> <p>Phylogenetic distribution<ul><li>eukarya mRNA</li></ul></p>
synonyms:
- m3Um
- σ
- 3,2'-O-dimethyluridine
identifiers:
- ns: rnamods
id: '92'
- ns: modomics.new_nomenclature
id: 03U
- ns: cas
id: 7103-27-7
- ns: modomics.short_name
id: m3Um
structure: COC1[C@@H](O)[C@H](O[C@H]1n1ccc(=O)n(c1=O)C)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
308U:
id: 308U
name: 3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine
synonyms:
- Ð
identifiers:
- ns: modomics.short_name
id: acp3D
- ns: modomics.new_nomenclature
id: 308U
structure: '[O-]C(=O)C(CCN1C(=O)CCN(C1=O)C1OC(C(C1O)O)COP(=O)([O-])[O-])[NH3+]'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 21
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 21
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
309U:
id: 309U
name: 3-(3-amino-3-carboxypropyl)pseudouridine
synonyms:
- Þ
identifiers:
- ns: modomics.new_nomenclature
id: 309U
- ns: modomics.short_name
id: acp3Y
structure: '[O-]C(=O)C(CCn1c(=O)[nH]cc(c1=O)C1OC(C(C1O)O)COP(=O)([O-])[O-])[NH3+]'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 22
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
30U:
id: 30U
name: 3-(3-amino-3-carboxypropyl)uridine
comments: <p>Earlier symbols used were 4abu3U and X. Symbol X for acp3U has been
confused in the literature with "unknown nucleoside" and its use is therefore
discouraged.</p> <p>Phylogenetic distribution<ul><li>bacteria tRNA</li><li>archaea
rRNA</li></ul></p>
synonyms:
- acp3U
- X
identifiers:
- ns: modomics.short_name
id: acp3U
- ns: rnamods
id: '61'
- ns: cas
id: 52745-94-5
- ns: modomics.new_nomenclature
id: 30U
structure: '[O-]C(=O)C(CCn1c(=O)ccn(c1=O)C1OC(C(C1O)O)COP(=O)([O-])[O-])[NH3+]'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 21
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 21
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
3C:
id: 3C
name: 3-methylcytidine
comments: <p></p> <p>Phylogenetic distribution<ul><li>bacteria tRNA</li><li>eukarya
tRNA</li><li>eukarya rRNA</li></ul></p>
synonyms:
- "'"
- m3C
identifiers:
- ns: rnamods
id: '20'
- ns: cas
id: 2140-64-9
- ns: pubchem.compound
id: '159649'
- ns: modomics.new_nomenclature
id: 3C
- ns: modomics.short_name
id: m3C
structure: OC1[C@@H](O)[C@H](O[C@H]1n1ccc([n+](c1=O)C)N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 22
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
39U:
id: 39U
name: 3-methylpseudouridine
comments: <p>Preparation of m3Y was reported in as one of several products formed
by reaction of Y with diazomethane; however, the structure assignment of the
synthetic material was regarded as tentative.</p> <p>Phylogenetic distribution<ul><li>bacteria
rRNA</li></ul></p>
synonyms:
- κ
- m3Y
identifiers:
- ns: rnamods
id: '94'
- ns: modomics.new_nomenclature
id: 39U
- ns: cas
id: 81691-06-7
- ns: modomics.short_name
id: m3Y
structure: OC1C(O)C(OC1c1c[nH]c(=O)n(c1=O)C)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 20
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
3U:
id: 3U
name: 3-methyluridine
comments: <p>Verification that the early report of m3U synthesis was correct was
made much later. Although this nucleoside was reported present in both 18S and
28S rRNA from HeLa cells, later studies showed it to be confined to the 28S
rRNA.</p> <p>Phylogenetic distribution<ul><li>archaea rRNA</li><li>bacteria
rRNA</li><li>eukarya rRNA</li></ul></p>
synonyms:
- 3-methyluridine-5'-monophoshate
- U
- m3U
- 3-methyluridine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
- δ
- UR3
identifiers:
- ns: pubchem.compound
id: '316991'
- ns: modomics.short_name
id: m3U
- ns: rnamods
id: '85'
- ns: modomics.new_nomenclature
id: 3U
- ns: cas
id: 2140-69-4
- ns: pdb-ccd
id: UR3
structure: O[C@H]1[C@@H](O)[C@H](O[C@H]1n1ccc(=O)n(c1=O)C)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
4G:
id: 4G
name: 4-demethylwyosine
comments: <p>Nomenclature for the yW family of nucleosides is discussed in and.
Numbering is based on 1H-imidazo[1,2-a]purine.</p> <p>Phylogenetic distribution<ul><li>archaea
tRNA</li></ul></p>
synonyms:
- imG-14
- †
identifiers:
- ns: modomics.new_nomenclature
id: 4G
- ns: rnamods
id: '100'
- ns: cas
id: 59327-60-5
- ns: modomics.short_name
id: imG-14
- ns: pubchem.compound
id: '477875'
structure: OC1C(O)C(OC1n1cnc2c1[nH]c1nc(cn1c2=O)C)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
74U:
id: 74U
name: 4-thiouridine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria
tRNA</li></ul></p>
synonyms:
- '4'
- U
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-oxo-4-sulfanylidene-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- s4U
- 4-thiouridine-5'-monophosphate
- 1-(5-O-phosphono-beta-D-ribofuranosyl)-4-thioxo-3,4-dihydropyrimidin-2(1H)-one
- 4SU
identifiers:
- ns: pubchem.compound
id: '3954028'
- ns: modomics.short_name
id: s4U
- ns: modomics.new_nomenclature
id: 74U
- ns: cas
id: 13957-31-8
- ns: rnamods
id: '58'
- ns: pdb-ccd
id: 4SU
structure: O[C@H]1[C@H](O)[C@@H](O[C@H]1n1ccc(=S)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
05C:
id: 05C
name: 5,2′-O-dimethylcytidine
comments: <p>Preliminary communication of structural characterization and chemical
synthesis is given in.</p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li></ul></p>
synonyms:
- 5,2'-O-dimethylcytidine
- τ
- m5Cm
identifiers:
- ns: rnamods
id: '26'
- ns: modomics.new_nomenclature
id: 05C
- ns: modomics.short_name
id: m5Cm
- ns: cas
id: 113886-70-7
structure: COC1C(O)C(OC1n1cc(C)c(nc1=O)N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 20
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
05U:
id: 05U
name: 5,2′-O-dimethyluridine
comments: <p>Alternate symbol is Tm.</p> <p>Phylogenetic distribution<ul><li>eukarya
tRNA</li></ul></p>
synonyms:
- m5Um
- 2',5-dimethyluridine-5'-monophosphate
- \
- '[(2R,3R,4R,5R)-3-hydroxy-4-methoxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- 5,2'-O-dimethyluridine
- 2MU
- U
- 5-methyl-2'-O-methyluridine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 2MU
- ns: cas
id: 55486-09-4
- ns: rnamods
id: '54'
- ns: modomics.short_name
id: m5Um
- ns: modomics.new_nomenclature
id: 05U
structure: CO[C@H]1[C@H](O)[C@@H](O[C@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 7
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 7
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
0522U:
id: 0522U
name: 5-(carboxyhydroxymethyl)-2′-O-methyluridine methyl ester
synonyms:
- b
identifiers:
- ns: modomics.short_name
id: mchm5Um
- ns: modomics.new_nomenclature
id: 0522U
structure: COC1[C@@H](O)[C@H](O[C@H]1n1cc(c(=O)[nH]c1=O)C(C(=O)OC)O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 29
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 32
charge: -1
522U:
id: 522U
name: 5-(carboxyhydroxymethyl)uridine methyl ester
comments: <p></p> <p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- mchm5U
- ','
identifiers:
- ns: rnamods
id: '67'
- ns: modomics.short_name
id: mchm5U
- ns: modomics.new_nomenclature
id: 522U
- ns: cas
id: 89665-83-8
structure: COC(=O)C(c1cn(c(=O)[nH]c1=O)C1OC(C(C1O)O)COP(=O)([O-])[O-])O
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 21
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 21
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
2583U:
id: 2583U
name: 5-(isopentenylaminomethyl)-2-thiouridine
comments: '<p>Preparation of conventional manuscript is in progress. Source of
tRNA: Thermodesulfobacterium commune. Coautors for this work: Phillips, D.R.,
Hashizume, T., Crain, P.F., Widdel, F.</p> <p>Phylogenetic distribution<ul><li>bacteria
tRNA</li></ul></p>'
synonyms:
- inm5s2U
- 5-(isopentenylaminomethyl)- 2-thiouridine
- ½
identifiers:
- ns: rnamods
id: '104'
- ns: modomics.short_name
id: inm5s2U
- ns: cas
id: 872710-78-6
- ns: modomics.new_nomenclature
id: 2583U
structure: CC(=CC[NH2+]Cc1cn(c(=S)[nH]c1=O)C1OC(C(C1O)O)COP(=O)([O-])[O-])C
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 24
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 24
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
0583U:
id: 0583U
name: 5-(isopentenylaminomethyl)-2′-O-methyluridine
comments: '<p>Preparation of conventional manuscript is in progress. Source of
tRNA: Thermodesulfobacterium commune. Coautors for this work: Phillips, D.R.,
Hashizume, T., Crain, P.F., Widdel, F.</p> <p>Phylogenetic distribution<ul><li>bacteria
tRNA</li></ul></p>'
synonyms:
- inm5Um
- ¼
- 5-(isopentenylaminomethyl)- 2'-O-methyluridine
identifiers:
- ns: cas
id: 872710-80-0
- ns: rnamods
id: '105'
- ns: modomics.new_nomenclature
id: 0583U
- ns: modomics.short_name
id: inm5Um
structure: COC1C(O)C(OC1n1cc(C[NH2+]CC=C(C)C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 29
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 32
charge: -1
583U:
id: 583U
name: 5-(isopentenylaminomethyl)uridine
comments: '<p>Preparation of conventional manuscript is in progress. Source of
tRNA: Thermodesulfobacterium commune. Coautors for this work: Phillips, D.R.,
Hashizume, T., Crain, P.F., Widdel, F.</p> <p>Phylogenetic distribution<ul><li>bacteria
tRNA</li></ul></p>'
synonyms:
- ¾
- inm5U
identifiers:
- ns: modomics.new_nomenclature
id: 583U
- ns: modomics.short_name
id: inm5U
- ns: rnamods
id: '103'
- ns: cas
id: 872710-76-4
structure: CC(=CC[NH2+]Cc1cn(c(=O)[nH]c1=O)C1OC(C(C1O)O)COP(=O)([O-])[O-])C
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 24
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 24
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
21510U:
id: 21510U
name: 5-aminomethyl-2-geranylthiouridine
synonyms:
- Δ
identifiers:
- ns: modomics.new_nomenclature
id: 21510U
- ns: modomics.short_name
id: nm5ges2U
structure: '[NH3+]Cc1cn(c(nc1=O)SC/C=C(/CCC=C(C)C)\C)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 33
l_bond_atoms:
- molecule: Monomer
element: P
position: 36
r_displaced_atoms:
- molecule: Monomer
element: H
position: 33
l_displaced_atoms:
- molecule: Monomer
element: O
position: 39
charge: -1
20510U:
id: 20510U
name: 5-aminomethyl-2-selenouridine
synonyms:
- π
identifiers:
- ns: modomics.new_nomenclature
id: 20510U
- ns: modomics.short_name
id: nm5se2U
structure: '[NH3+]Cc1cn(c(=[Se])[nH]c1=O)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 24
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 24
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
2510U:
id: 2510U
name: 5-aminomethyl-2-thiouridine
comments: <p>Observed as a component of unfractionated tRNA from E. coli mutants,
as a biosynthetic precursor to mnm5s2U; not rigorously characterized by conventional
means. No chemical synthesis reported.</p> <p>Phylogenetic distribution<ul><li>bacteria
tRNA</li></ul></p>
synonyms:
- ∫
- nm5s2U
identifiers:
- ns: modomics.new_nomenclature
id: 2510U
- ns: modomics.short_name
id: nm5s2U
- ns: cas
id: 109666-14-0
- ns: rnamods
id: '71'
structure: '[NH3+]Cc1cn(c(=S)[nH]c1=O)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 24
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 24
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
510U:
id: 510U
name: 5-aminomethyluridine
synonyms:
- ∪
identifiers:
- ns: modomics.new_nomenclature
id: 510U
- ns: modomics.short_name
id: nm5U
structure: '[NH3+]Cc1cn(c(=O)[nH]c1=O)C1OC(C(C1O)O)COP(=O)([O-])[O-]'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 21
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 21
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
531U:
id: 531U
name: 5-carbamoylhydroxymethyluridine
synonyms:
- r
identifiers:
- ns: modomics.short_name
id: nchm5U
- ns: modomics.new_nomenclature
id: 531U
structure: NC(=O)C(c1cn(c(=O)[nH]c1=O)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-])O
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 23
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
r_displaced_atoms:
- molecule: Monomer
element: H
position: 23
l_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
253U:
id: 253U
name: 5-carbamoylmethyl-2-thiouridine
synonyms:
- l
identifiers:
- ns: modomics.new_nomenclature
id: 253U
- ns: modomics.short_name
id: ncm5s2U
structure: NC(=O)Cc1cn(c(=S)[nH]c1=O)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 23
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
r_displaced_atoms:
- molecule: Monomer
element: H
position: 23
l_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
053U:
id: 053U
name: 5-carbamoylmethyl-2′-O-methyluridine
comments: <p>The first preparation of ncm5Um was by conversion of cm5Um which
had been isolated from tRNA in the same study. Conventional chemical synthesis
of ncm5Um is reported in.</p> <p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- ncm5Um
- '~'
- 5-carbamoylmethyl-2'-O-methyluridine
identifiers:
- ns: rnamods
id: '76'
- ns: modomics.short_name
id: ncm5Um
- ns: modomics.new_nomenclature
id: 053U
- ns: cas
id: 60197-30-0
structure: COC1C(O)C(OC1n1cc(CC(=O)N)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
53U:
id: 53U
name: 5-carbamoylmethyluridine
comments: <p></p> <p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- ncm5U
- '&'
identifiers:
- ns: modomics.short_name
id: ncm5U
- ns: cas
id: 29569-30-0
- ns: modomics.new_nomenclature
id: 53U
- ns: rnamods
id: '75'
structure: NC(=O)Cc1cn(c(=O)[nH]c1=O)C1OC(C(C1O)O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 20
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 20
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
520U:
id: 520U
name: 5-carboxyhydroxymethyluridine
comments: <p>The Chemical Abstracts registry number listed is for the natural
(S)-isomer; the (R)-isomer registry number is 127911-55-1.</p> <p>Phylogenetic
distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- 5-(carboxyhydroxymethyl)uridine
- ≥
- chm5U
identifiers:
- ns: cas
id: 89708-80-5
- ns: modomics.new_nomenclature
id: 520U
- ns: modomics.short_name
id: chm5U
- ns: rnamods
id: '66'
structure: '[O-]C(=O)C(c1cn(c(=O)[nH]c1=O)C1OC(C(C1O)O)COP(=O)([O-])[O-])O'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 20
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 20
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
2540U:
id: 2540U
name: 5-carboxymethyl-2-thiouridine
synonyms:
- ℘
identifiers:
- ns: modomics.new_nomenclature
id: 2540U
- ns: modomics.short_name
id: cm5s2U
structure: '[O-]C(=O)Cc1cn(c(=S)[nH]c1=O)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 23
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
r_displaced_atoms:
- molecule: Monomer
element: H
position: 23
l_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
2151U:
id: 2151U
name: 5-carboxymethylaminomethyl-2-geranylthiouridine
comments: <p>None</p> <p>Phylogenetic distribution<ul><li></li></ul></p>
synonyms:
- f
- geranylated 5-carboxymethylaminomethyl-2-thiouridine
- gcmnm5s2U
identifiers:
- ns: modomics.new_nomenclature
id: 2151U
- ns: modomics.short_name
id: cmnm5ges2U
- ns: cas
id: 1401688-11-6
- ns: rnamods
id: '119'
structure: '[O-]C(=O)C[NH2+]Cc1cn(c(nc1=O)SC/C=C(/CCC=C(C)C)\C)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 36
l_bond_atoms:
- molecule: Monomer
element: P
position: 39
r_displaced_atoms:
- molecule: Monomer
element: H
position: 36
l_displaced_atoms:
- molecule: Monomer
element: O
position: 42
charge: -1
2051U:
id: 2051U
name: 5-carboxymethylaminomethyl-2-selenouridine
synonyms:
- ⊥
identifiers:
- ns: modomics.short_name
id: cmnm5se2U
- ns: modomics.new_nomenclature
id: 2051U
structure: '[O-]C(=O)C[NH2+]Cc1cn(c(=[Se])[nH]c1=O)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 27
l_bond_atoms:
- molecule: Monomer
element: P
position: 30
r_displaced_atoms:
- molecule: Monomer
element: H
position: 27
l_displaced_atoms:
- molecule: Monomer
element: O
position: 33
charge: -1
251U:
id: 251U
name: 5-carboxymethylaminomethyl-2-thiouridine
comments: <p>Alternate symbol is cmam5s2U.</p> <p>Phylogenetic distribution<ul><li>bacteria
tRNA</li></ul></p>
synonyms:
- $
- cmnm5s2U
identifiers:
- ns: modomics.short_name
id: cmnm5s2U
- ns: modomics.new_nomenclature
id: 251U
- ns: cas
id: 78173-95-2
- ns: pubchem.compound
id: '3037867'
- ns: rnamods
id: '79'
structure: '[O-]C(=O)C[NH2+]Cc1cn(c(=S)[nH]c1=O)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 27
l_bond_atoms:
- molecule: Monomer
element: P
position: 30
r_displaced_atoms:
- molecule: Monomer
element: H
position: 27
l_displaced_atoms:
- molecule: Monomer
element: O
position: 33
charge: -1
051U:
id: 051U
name: 5-carboxymethylaminomethyl-2′-O-methyluridine
comments: <p>Alternate symbol is cmam5Um. The natural nucleoside from E. coli
tRNALeu was originally characterized by comparison of its NMR spectrum with
that of synthetic material. The discovery of cmnm5Um is cited in as a meeting
abstract, in which, however, the compound is neither named nor structural data
presented. A recent and more rigorous structural characterization is reported
in.</p> <p>Phylogenetic distribution<ul><li>bacteria tRNA</li></ul></p>
synonyms:
- 5-carboxymethylaminomethyl- 2'-O-methyluridine
- )
- cmnm5Um
identifiers:
- ns: cas
id: 110419-13-1
- ns: modomics.short_name
id: cmnm5Um
- ns: modomics.new_nomenclature
id: 051U
- ns: rnamods
id: '78'
structure: COC1C(O)C(OC1n1cc(C[NH2+]CC(=O)[O-])c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 28
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 31
charge: -1
51U:
id: 51U
name: 5-carboxymethylaminomethyluridine
comments: <p>Alternate symbol is cmam5U.</p> <p>Phylogenetic distribution<ul><li>bacteria
tRNA</li><li>eukarya tRNA</li></ul></p>
synonyms:
- cmnm5U
- '!'
identifiers:
- ns: rnamods
id: '77'
- ns: modomics.short_name
id: cmnm5U
- ns: modomics.new_nomenclature
id: 51U
- ns: pubchem.compound
id: '194306'
- ns: cas
id: 69181-26-6
structure: '[O-]C(=O)C[NH2+]Cc1cn(c(=O)[nH]c1=O)C1OC(C(C1O)O)COP(=O)([O-])[O-]'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 24
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 24
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
52U:
id: 52U
name: 5-carboxymethyluridine
comments: <p>5-(Hydroxymethyl)cytidine and 5-(carboxymethyl)uridine were identified
as the monophosphates by their UV spectra following separation by 2D-TLC (data
not shown); however, availability of authentic compounds or of previously cited
properties was not addressed. These structure assignments are therefore considered
inconclusive.</p> <p>Phylogenetic distribution<ul><li>eukarya rRNA</li></ul></p>
synonyms:
- ◊
- cm5U
identifiers:
- ns: pubchem.compound
id: '3080720'
- ns: modomics.short_name
id: cm5U
- ns: cas
id: 20964-06-1
- ns: modomics.new_nomenclature
id: 52U
- ns: rnamods
id: '87'
structure: '[O-]C(=O)Cc1cn(c(=O)[nH]c1=O)C1OC(C(C1O)O)COP(=O)([O-])[O-]'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 20
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 20
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
55U:
id: 55U
name: 5-cyanomethyluridine
comments: <p>None</p> <p>Phylogenetic distribution<ul><li></li></ul></p>
synonyms:
- cnm5U
- Ѷ
- 5-cyanomethyl-uridine
identifiers:
- ns: cas
id: 58479-73-5
- ns: modomics.new_nomenclature
id: 55U
- ns: rnamods
id: '120'
- ns: modomics.short_name
id: cnm5U
structure: N#CCc1cn(c(=O)[nH]c1=O)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 22
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
071C:
id: 071C
name: 5-formyl-2′-O-methylcytidine
comments: <p></p> <p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- °
- f5Cm
- 5-formyl-2'-O-methylcytidine
identifiers:
- ns: rnamods
id: '95'
- ns: modomics.short_name
id: f5Cm
- ns: modomics.new_nomenclature
id: 071C
- ns: cas
id: 176858-79-0
structure: COC1C(O)C(OC1n1cc(C=O)c(nc1=O)N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 21
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
71C:
id: 71C
name: 5-formylcytidine
comments: <p></p> <p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- 5-formylcytidine 5'-(dihydrogen phosphate)
- RSQ
- '[(2R,3S,4R,5R)-5-(4-azanyl-5-methanoyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
- f5C
- '>'
identifiers:
- ns: modomics.short_name
id: f5C
- ns: modomics.new_nomenclature
id: 71C
- ns: pdb-ccd
id: RSQ
- ns: cas
id: 148608-53-1
- ns: rnamods
id: '25'
structure: O=Cc1cn(c(=O)nc1N)[C@H]1O[C@H]([C@@H]([C@@H]1O)O)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 21
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 21
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
50C:
id: 50C
name: 5-hydroxycytidine
synonyms:
- Ç
identifiers:
- ns: modomics.new_nomenclature
id: 50C
- ns: modomics.short_name
id: ho5C
structure: OC1C(O)C(OC1n1cc(O)c(nc1=O)N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 19
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 22
charge: -1
51C:
id: 51C
name: 5-hydroxymethylcytidine
comments: <p>5-(Hydroxymethyl)cytidine and 5-(carboxymethyl)uridine were identified
as the monophosphates by their UV spectra following separation by 2D-TLC (data
not shown); however, availability of authentic compounds or of previously cited
properties was not addressed. These structure assignments are therefore considered
inconclusive.</p> <p>Phylogenetic distribution<ul><li>eukarya rRNA</li></ul></p>
synonyms:
- ∅
- hm5C
identifiers:
- ns: modomics.short_name
id: hm5C
- ns: cas
id: 19235-17-7
- ns: rnamods
id: '84'
- ns: modomics.new_nomenclature
id: 51C
structure: OCc1cn(c(=O)nc1N)C1OC(C(C1O)O)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 17
l_bond_atoms:
- molecule: Monomer
element: P
position: 20
r_displaced_atoms:
- molecule: Monomer
element: H
position: 17
l_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
50U:
id: 50U
name: 5-hydroxyuridine
comments: <p></p> <p>Phylogenetic distribution<ul><li>bacteria tRNA</li><li>eukarya
tRNA</li></ul></p>
synonyms:
- ∝
- ho5U
identifiers:
- ns: modomics.new_nomenclature
id: 50U
- ns: modomics.short_name
id: ho5U
- ns: rnamods
id: '62'
- ns: cas
id: 957-77-7
structure: OC1C(O)C(OC1n1cc(O)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 20
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
2521U:
id: 2521U
name: 5-methoxycarbonylmethyl-2-thiouridine
comments: <p></p> <p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- 5-(o-methylaceto)-2-thio-2-deoxy-uridine-5'-monophosphate
- 5-(2-methoxy-2-oxoethyl)-1-(5-O-phosphono-beta-D-ribofuranosyl)-2-thioxo-2,3-dihydropyrimidin-4(1H)-one
- 70U
- mcm5s2U
- U
- '3'
- methyl 2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-4-oxo-2-sulfanylidene-pyrimidin-5-yl]ethanoate
identifiers:
- ns: pdb-ccd
id: 70U
- ns: rnamods
id: '70'
- ns: modomics.new_nomenclature
id: 2521U
- ns: modomics.short_name
id: mcm5s2U
- ns: cas
id: 20299-15-4
structure: COC(=O)Cc1cn(c(=S)[nH]c1=O)[C@@H]1O[C@H]([C@@H]([C@@H]1O)O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 25
l_bond_atoms:
- molecule: Monomer
element: P
position: 28
r_displaced_atoms:
- molecule: Monomer
element: H
position: 25
l_displaced_atoms:
- molecule: Monomer
element: O
position: 31
charge: -1
0521U:
id: 0521U
name: 5-methoxycarbonylmethyl-2′-O-methyluridine
comments: <p></p> <p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- ∩
- 5-methoxycarbonylmethyl-2'-O-methyluridine
- mcm5Um
identifiers:
- ns: modomics.short_name
id: mcm5Um
- ns: cas
id: 60197-31-1
- ns: rnamods
id: '69'
- ns: modomics.new_nomenclature
id: 0521U
structure: COC1C(O)C(OC1n1cc(CC(=O)OC)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
521U:
id: 521U
name: 5-methoxycarbonylmethyluridine
comments: <p></p> <p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- '1'
- mcm5U
identifiers:
- ns: cas
id: 29428-50-0
- ns: modomics.short_name
id: mcm5U
- ns: rnamods
id: '68'
- ns: modomics.new_nomenclature
id: 521U
structure: COC(=O)Cc1cn(c(=O)[nH]c1=O)C1OC(C(C1O)O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 21
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 21
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
501U:
id: 501U
name: 5-methoxyuridine
comments: <p></p> <p>Phylogenetic distribution<ul><li>bacteria tRNA</li></ul></p>
synonyms:
- '5'
- mo5U
identifiers:
- ns: cas
id: 35542-01-9
- ns: modomics.short_name
id: mo5U
- ns: modomics.new_nomenclature
id: 501U
- ns: rnamods
id: '63'
- ns: pubchem.compound
id: '169704'
structure: COc1cn(c(=O)[nH]c1=O)C1OC(C(C1O)O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 18
l_bond_atoms:
- molecule: Monomer
element: P
position: 21
r_displaced_atoms:
- molecule: Monomer
element: H
position: 18
l_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
25U:
id: 25U
name: 5-methyl-2-thiouridine
comments: <p>Alternate symbol is s2T. The occurrence of m5s2U in archaeal tRNA
is unusual.</p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria
tRNA</li><li>eukarya tRNA</li></ul></p>
synonyms:
- F
- m5s2U
identifiers:
- ns: pubchem.compound
id: '3035361'
- ns: cas
id: 32738-09-3
- ns: modomics.short_name
id: m5s2U
- ns: rnamods
id: '59'
- ns: modomics.new_nomenclature
id: 25U
structure: OC1[C@@H](O)[C@H](O[C@H]1n1cc(C)c(=O)[nH]c1=S)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
21511U:
id: 21511U
name: 5-methylaminomethyl-2-geranylthiouridine
comments: <p>None</p> <p>Phylogenetic distribution<ul><li></li></ul></p>
synonyms:
- geranylated 5-methylaminomethyl-2-thiouridine
- gmnm5s2U
- h
identifiers:
- ns: cas
id: 1401688-10-5
- ns: rnamods
id: '118'
- ns: modomics.new_nomenclature
id: 21511U
- ns: modomics.short_name
id: mnm5ges2U
structure: C[NH2+]Cc1cn(c(nc1=O)SC/C=C(/CCC=C(C)C)\C)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 33
l_bond_atoms:
- molecule: Monomer
element: P
position: 36
r_displaced_atoms:
- molecule: Monomer
element: H
position: 33
l_displaced_atoms:
- molecule: Monomer
element: O
position: 39
charge: -1
20511U:
id: 20511U
name: 5-methylaminomethyl-2-selenouridine
comments: <p>Earlier reports of se4U in RNA cited in were discounted, as discussed
in. Although only one selenonucleoside, mnm5se2U, has been structurally characterized,
it is likely that others exist but have not been detected due to oxidation,
for example, in eukaryotic tRNA.</p> <p>Phylogenetic distribution<ul><li>archaea
tRNA</li><li>bacteria tRNA</li></ul></p>
synonyms:
- mnm5se2U
- ≅
identifiers:
- ns: rnamods
id: '74'
- ns: cas
id: 89314-80-7
- ns: modomics.new_nomenclature
id: 20511U
- ns: pubchem.compound
id: '6336326'
- ns: modomics.short_name
id: mnm5se2U
structure: C[NH2+]Cc1cn(c(=[Se])[nH]c1=O)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 24
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 24
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
2511U:
id: 2511U
name: 5-methylaminomethyl-2-thiouridine
comments: <p>Alternate symbol is mam5s2U.</p> <p>Phylogenetic distribution<ul><li>archaea
tRNA</li><li>bacteria tRNA</li></ul></p>
synonyms:
- S
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-[5-(methylaminomethyl)-4-oxo-2-sulfanylidene-pyrimidin-1-yl]oxolan-2-yl]methyl
dihydrogen phosphate'
- U
- 5-[(methylamino)methyl]-1-(5-O-phosphono-beta-D-ribofuranosyl)-2-thioxo-2,3-dihydropyrimidin-4(1H)-one
- U8U
- 5-methylaminomethyl-2-thiouridine-5'-monophosphate
- mnm5s2U
identifiers:
- ns: rnamods
id: '73'
- ns: pdb-ccd
id: U8U
- ns: modomics.short_name
id: mnm5s2U
- ns: modomics.new_nomenclature
id: 2511U
- ns: pubchem.compound
id: '3036488'
- ns: cas
id: 32860-54-1
structure: CNCc1cn(c(=S)[nH]c1=O)[C@@H]1O[C@H]([C@@H]([C@@H]1O)O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 23
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
r_displaced_atoms:
- molecule: Monomer
element: H
position: 23
l_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
511U:
id: 511U
name: 5-methylaminomethyluridine
comments: <p>Alternate symbol is mam5U. More thorough characterization in.</p>
<p>Phylogenetic distribution<ul><li>bacteria tRNA</li></ul></p>
synonyms:
- 5-[(methylamino)methyl]uridine 5'-(dihydrogen phosphate)
- U
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-[5-(methylaminomethyl)-2,4-dioxo-pyrimidin-1-yl]oxolan-2-yl]methyl
dihydrogen phosphate'
- MNU
- '{'
- mnm5U
- (2r,4s)-1-[(4r)-3,4-dihydroxytetrahydrofuran-2-yl]-5-[(methylamino)methyl]-1,2,3,4-tetrahydropyrimidine-2,4-diol-5'-monophosphate
identifiers:
- ns: modomics.new_nomenclature
id: 511U
- ns: modomics.short_name
id: mnm5U
- ns: pdb-ccd
id: MNU
- ns: rnamods
id: '72'
- ns: cas
id: 72667-55-1
structure: CNCc1cn(c(=O)[nH]c1=O)[C@@H]1O[C@@H]([C@@H]([C@@H]1O)O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 23
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
r_displaced_atoms:
- molecule: Monomer
element: H
position: 23
l_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
5C:
id: 5C
name: 5-methylcytidine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>eukarya
tRNA</li><li>archaea rRNA</li><li>bacteria rRNA</li><li>eukarya rRNA</li><li>eukarya
mRNA</li></ul></p>
synonyms:
- m5C
- 5MC
- C
- '?'
- 5-methylcytidine-5'-monophosphate
- 5-methylcytidine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-5-(4-amino-5-methyl-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: cas
id: 2140-61-6
- ns: rnamods
id: '21'
- ns: pdb-ccd
id: 5MC
- ns: pubchem.compound
id: '92918'
- ns: modomics.short_name
id: m5C
- ns: modomics.new_nomenclature
id: 5C
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cc(C)c(nc1=O)N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
58U:
id: 58U
name: 5-methyldihydrouridine
comments: <p>This RNA is reported as a chromatin-associated 3.2-3.8S species,
with an unusual concentration of dihydropyrimidine nucleosides, but its occurrence
as a separate class of RNA remains controversial. For review, see. Characterization
of this nucleoside, not otherwise reported in RNA, was based on detection of
2-amino-isobutyric acid following treatment with alkali. Direct comparison with
the authentic nucleoside was not made.</p> <p>Phylogenetic distribution<ul><li>eukarya
chromosomal RNA</li></ul></p>
synonyms:
- ρ
- m5D
identifiers:
- ns: rnamods
id: '93'
- ns: cas
id: 23067-10-9
- ns: modomics.new_nomenclature
id: 58U
- ns: modomics.short_name
id: m5D
structure: OC1C(O)C(OC1N1CC(C)C(=O)NC1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 19
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 22
charge: -1
5U:
id: 5U
name: 5-methyluridine
comments: <p>Alternate commonly used symbol is T. Other common names are thymine
riboside and ribosylthymine. Occurrence is rare in archaeal tRNA. Enzymatic
synthesis was reported in, which preceded the first report of chemical synthesis.</p>
<p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria tRNA</li><li>eukarya
tRNA</li><li>bacteria rRNA</li><li>bacteria tmRNA</li></ul></p>
synonyms:
- m5U
- 5MU
- T
- U
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- 5-methyluridine 5'-(dihydrogen phosphate)
- 5-methyluridine 5'-monophosphate
identifiers:
- ns: modomics.new_nomenclature
id: 5U
- ns: pubchem.compound
id: '445408'
- ns: modomics.short_name
id: m5U
- ns: pdb-ccd
id: 5MU
- ns: rnamods
id: '52'
- ns: cas
id: 1463-10-1
structure: O[C@H]1[C@H](O)[C@@H](O[C@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
254U:
id: 254U
name: 5-taurinomethyl-2-thiouridine
comments: <p>Alternate symbol is taum5s2U. See also</p> <p>Phylogenetic distribution<ul><li>eukarya
tRNA</li></ul></p>
synonyms:
- tm5s2U
- ∃
identifiers:
- ns: modomics.new_nomenclature
id: 254U
- ns: modomics.short_name
id: tm5s2U
- ns: rnamods
id: '99'
- ns: cas
id: 497258-54-5
structure: OC1[C@@H](O)[C@H](O[C@H]1n1cc(C[NH2+]CCS(=O)(=O)[O-])c(=O)[nH]c1=S)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 32
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 35
charge: -1
54U:
id: 54U
name: 5-taurinomethyluridine
comments: <p>Alternate symbol is tau5U. See also</p> <p>Phylogenetic distribution<ul><li>eukarya
tRNA</li></ul></p>
synonyms:
- Ê
- tm5U
identifiers:
- ns: modomics.new_nomenclature
id: 54U
- ns: rnamods
id: '98'
- ns: modomics.short_name
id: tm5U
- ns: cas
id: 497258-53-4
structure: OC1C(O)C(OC1n1cc(C[NH2+]CCS(=O)(=O)[O-])c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 29
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 32
charge: -1
47G:
id: 47G
name: 7-aminocarboxypropyl-demethylwyosine
synonyms:
- ¥
identifiers:
- ns: modomics.new_nomenclature
id: 47G
- ns: modomics.short_name
id: yW-86
structure: '[O-]C(=O)C(CCc1c(C)nc2n1c(=O)c1c([nH]2)n(cn1)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-])[NH3+]'
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 31
l_bond_atoms:
- molecule: Monomer
element: P
position: 34
r_displaced_atoms:
- molecule: Monomer
element: H
position: 31
l_displaced_atoms:
- molecule: Monomer
element: O
position: 37
charge: -1
347G:
id: 347G
name: 7-aminocarboxypropylwyosine
synonyms:
- Ω
identifiers:
- ns: modomics.new_nomenclature
id: 347G
- ns: modomics.short_name
id: yW-72
structure: '[O-]C(=O)C(CCc1c(C)nc2n1c(=O)c1c(n2C)n(cn1)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-])[NH3+]'
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 31
l_bond_atoms:
- molecule: Monomer
element: P
position: 34
r_displaced_atoms:
- molecule: Monomer
element: H
position: 31
l_displaced_atoms:
- molecule: Monomer
element: O
position: 37
charge: -1
348G:
id: 348G
name: 7-aminocarboxypropylwyosine methyl ester
synonyms:
- ⇑
identifiers:
- ns: modomics.new_nomenclature
id: 348G
- ns: modomics.short_name
id: yW-58
structure: COC(=O)C(CCc1c(C)nc2n1c(=O)c1c(n2C)n(cn1)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-])[NH3+]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 32
l_bond_atoms:
- molecule: Monomer
element: P
position: 35
r_displaced_atoms:
- molecule: Monomer
element: H
position: 32
l_displaced_atoms:
- molecule: Monomer
element: O
position: 38
charge: -1
101G:
id: 101G
name: 7-aminomethyl-7-deazaguanosine
comments: <p>preQ0 and preQ1 are undermodified Q nucleosides isolated from methyl-deficient
mutant E. coli tRNA.</p> <p>Phylogenetic distribution<ul><li>bacteria tRNA</li></ul></p>
synonyms:
- ∉
- preQ1
identifiers:
- ns: cas
id: 66048-70-2
- ns: modomics.new_nomenclature
id: 101G
- ns: rnamods
id: '48'
- ns: modomics.short_name
id: preQ1tRNA
structure: '[NH3+]Cc1cn(c2c1c(=O)[nH]c(n2)N)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]'
r_bond_atoms:
- molecule: Monomer
element: O
position: 27
l_bond_atoms:
- molecule: Monomer
element: P
position: 30
r_displaced_atoms:
- molecule: Monomer
element: H
position: 27
l_displaced_atoms:
- molecule: Monomer
element: O
position: 33
charge: -1
100G:
id: 100G
name: 7-cyano-7-deazaguanosine
comments: <p>preQ0 and preQ1 are undermodified Q nucleosides isolated from methyl-deficient
mutant E. coli tRNA.</p> <p>Phylogenetic distribution<ul><li>bacteria tRNA</li></ul></p>
synonyms:
- preQ0
- φ
identifiers:
- ns: modomics.short_name
id: preQ0tRNA
- ns: cas
id: 61210-21-7
- ns: modomics.new_nomenclature
id: 100G
- ns: rnamods
id: '47'
structure: N#Cc1cn(c2c1c(=O)[nH]c(n2)N)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 24
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 24
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
7G:
id: 7G
name: 7-methylguanosine
comments: <p>First characterized as the base and later as the monoribonucleotide.</p>
<p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria tRNA</li><li>eukarya
tRNA</li><li>archaea rRNA</li><li>bacteria rRNA</li><li>eukarya rRNA</li><li>eukarya
mRNA</li></ul></p>
synonyms:
- '7'
- m7G
identifiers:
- ns: rnamods
id: '31'
- ns: cas
id: 20244-86-4
- ns: modomics.short_name
id: m7G
- ns: modomics.new_nomenclature
id: 7G
structure: OC1[C@H](O)[C@@H](O[C@@H]1n1c[n+](c2c1N=C(N)NC2O)C)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
8A:
id: 8A
name: 8-methyladenosine
comments: <p>None</p> <p>Phylogenetic distribution<ul><li>bacteria rRNA</li></ul></p>
synonyms:
- m8A
- â
identifiers:
- ns: cas
id: 56973-12-7
- ns: rnamods
id: '114'
- ns: modomics.new_nomenclature
id: 8A
- ns: modomics.short_name
id: m8A
structure: OC1C(O)C(OC1n1c(C)nc2c1ncnc2N)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 21
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
02G:
id: 02G
name: N2,2′-O-dimethylguanosine
comments: <p>A preliminary report of characterization is given in.</p> <p>Phylogenetic
distribution<ul><li>archaea tRNA</li></ul></p>
synonyms:
- γ
- N2,2'-O-dimethylguanosine
- m2Gm
identifiers:
- ns: modomics.short_name
id: m2Gm
- ns: rnamods
id: '34'
- ns: cas
id: 135023-21-1
- ns: modomics.new_nomenclature
id: 02G
structure: COC1C(O)C(OC1n1cnc2c1nc(NC)[nH]c2=O)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
027G:
id: 027G
name: N2,7,2′-O-trimethylguanosine
comments: '<p>Sources of tRNA: Aeropyrum pernix, Stetteria hydrogenophila. See
also: Noon, K.R. et al. (2003) J. Bacteriol., 185, 5483-5490. Coauthors for
this work: Van Wagoner, R.M., Hashizume, T., Nomura, M., Sako, Y.</p> <p>Phylogenetic
distribution<ul><li>archaea tRNA</li></ul></p>'
synonyms:
- æ
- m2,7Gm
- N2,7,2'-O-trimethylguanosine
identifiers:
- ns: cas
id: 872710-82-2
- ns: modomics.new_nomenclature
id: 027G
- ns: modomics.short_name
id: m2,7Gm
- ns: rnamods
id: '106'
structure: COC1[C@H](O)[C@@H](O[C@@H]1n1c[n+](c2c1[NH+]=C(NC)NC2O)C)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 28
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 31
charge: -1
27G:
id: 27G
name: N2,7-dimethylguanosine
comments: <p>This 5'-cap nucleoside is joined to the RNA through a unique 3'-triphosphate
bridge (GpppN...).</p> <p>Phylogenetic distribution<ul><li>eukarya mRNA</li></ul></p>
synonyms:
- m2,7G
- ∨
identifiers:
- ns: modomics.short_name
id: m2,7G
- ns: rnamods
id: '90'
- ns: modomics.new_nomenclature
id: 27G
- ns: cas
id: 62122-07-0
structure: CNC1=[NH+]c2c(C(N1)O)[n+](cn2[C@H]1O[C@H]([C@H](C1O)O)COP(=O)([O-])[O-])C
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 23
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
r_displaced_atoms:
- molecule: Monomer
element: H
position: 23
l_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
022G:
id: 022G
name: N2,N2,2′-O-trimethylguanosine
comments: <p>Preliminary communication of structural characterization and chemical
synthesis is given in. Unknown nucleoside N-26 in Sulfolobus acidocaldarius
tRNAiMet was postulated to be m22Gm in, without experimental evidence.</p> <p>Phylogenetic
distribution<ul><li>archaea tRNA</li></ul></p>
synonyms:
- '|'
- m22Gm
- N2,N2,2'-O-trimethylguanosine
identifiers:
- ns: modomics.new_nomenclature
id: 022G
- ns: rnamods
id: '35'
- ns: cas
id: 113886-73-0
- ns: modomics.short_name
id: m2,2Gm
structure: COC1C(O)C(OC1n1cnc2c1nc([nH]c2=O)N(C)C)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
227G:
id: 227G
name: N2,N2,7-trimethylguanosine
comments: <p>The structure was first assigned using material from 2-10S RNA from
Chinese hamster ovary cells, and later from snRNA from Novikoff hepatoma ascites
cells. More rigorous characterization of the synthetic nucleoside used for comparison
is given in.</p> <p>Phylogenetic distribution<ul><li>eukarya mRNA</li><li>eukarya
snRNA</li></ul></p>
synonyms:
- ∠
- m2,2,7G
identifiers:
- ns: rnamods
id: '91'
- ns: modomics.new_nomenclature
id: 227G
- ns: modomics.short_name
id: m2,2,7G
- ns: cas
id: 40027-70-1
structure: OC1[C@H](O)[C@@H](O[C@@H]1n1c[n+](c2c1[NH+]=C(NC2O)N(C)C)C)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 28
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 31
charge: -1
22G:
id: 22G
name: N2,N2-dimethylguanosine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>eukarya
tRNA</li><li>bacteria rRNA</li><li>eukarya rRNA</li></ul></p>
synonyms:
- M2G
- G
- '[(2R,3S,4R,5R)-5-(2-dimethylamino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- m22G
- n2-dimethylguanosine-5'-monophosphate
- N,N-dimethylguanosine 5'-(dihydrogen phosphate)
- R
identifiers:
- ns: modomics.short_name
id: m2,2G
- ns: rnamods
id: '33'
- ns: cas
id: 2140-67-2
- ns: pubchem.compound
id: '601633'
- ns: modomics.new_nomenclature
id: 22G
- ns: pdb-ccd
id: M2G
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cnc2c1nc([nH]c2=O)N(C)C)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 28
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 31
charge: -1
2G:
id: 2G
name: N2-methylguanosine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>eukarya
tRNA</li><li>archaea rRNA</li><li>bacteria rRNA</li><li>eukarya rRNA</li><li>eukarya
snRNA</li></ul></p>
synonyms:
- L
- G
- 2n-methylguanosine-5'-monophosphate
- N-methylguanosine 5'-(dihydrogen phosphate)
- m2G
- 2MG
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-methylamino-6-oxo-1H-purin-9-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: cas
id: 2140-77-4
- ns: pubchem.compound
id: '3035422'
- ns: modomics.short_name
id: m2G
- ns: pdb-ccd
id: 2MG
- ns: rnamods
id: '30'
- ns: modomics.new_nomenclature
id: 2G
structure: CNc1[nH]c(=O)c2c(n1)n(cn2)[C@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 24
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 24
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
04C:
id: 04C
name: N4,2′-O-dimethylcytidine
comments: <p>More thorough characterization is reported in.</p> <p>Phylogenetic
distribution<ul><li>bacteria rRNA</li></ul></p>
synonyms:
- λ
- N-methyl-2'-O-methylcytidine 5'-(dihydrogen phosphate)
- C
- m4Cm
- '[(2R,3R,4R,5R)-3-hydroxy-4-methoxy-5-(4-methylamino-2-oxo-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- N4,2'-O-dimethylcytidine
- 4n,o2'-methylcytidine-5'-monophosphate
- 4OC
identifiers:
- ns: modomics.short_name
id: m4Cm
- ns: modomics.new_nomenclature
id: 04C
- ns: rnamods
id: '83'
- ns: cas
id: 13048-95-8
- ns: pdb-ccd
id: 4OC
structure: CO[C@H]1[C@H](O)[C@H](O[C@@H]1n1ccc(nc1=O)NC)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 7
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 7
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
044C:
id: 044C
name: N4,N4,2′-O-trimethylcytidine
comments: <p>Source of RNA, Aeropyrum pernix attributed to 16S rRNA although tRNA
cannot be rigorously excluded.</p> <p>Phylogenetic distribution<ul><li>archaea
tRNA</li></ul></p>
synonyms:
- m42Cm
- β
- N4,N4,2'-O-trimethylcytidine
identifiers:
- ns: modomics.short_name
id: m4,4Cm
- ns: modomics.new_nomenclature
id: 044C
- ns: rnamods
id: '107'
- ns: cas
id: 34218-81-0
structure: COC1C(O)C(OC1n1ccc(nc1=O)N(C)C)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 21
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
44C:
id: 44C
name: N4,N4-dimethylcytidine
synonyms:
- μ
identifiers:
- ns: pubchem.compound
id: '3082389'
- ns: modomics.new_nomenclature
id: 44C
- ns: modomics.short_name
id: m4,4C
structure: OC1C(O)C(OC1n1ccc(nc1=O)N(C)C)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 20
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
042C:
id: 042C
name: N4-acetyl-2′-O-methylcytidine
comments: <p>Preliminary communication of structural characterization and chemical
synthesis is given in.</p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>archaea
rRNA</li></ul></p>
synonyms:
- ℵ
- ac4Cm
- N4-acetyl-2'-O-methylcytidine
identifiers:
- ns: rnamods
id: '27'
- ns: modomics.new_nomenclature
id: 042C
- ns: modomics.short_name
id: ac4Cm
- ns: cas
id: 113886-71-8
structure: COC1C(O)C(OC1n1ccc(nc1=O)NC(=O)C)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 22
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
42C:
id: 42C
name: N4-acetylcytidine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria
tRNA</li><li>eukarya tRNA</li><li>archaea rRNA</li><li>eukarya rRNA</li></ul></p>
synonyms:
- '[(2R,3S,4R,5R)-5-(4-acetamido-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- N-acetylcytidine 5'-(dihydrogen phosphate)
- ac4C
- N
- M
- 4AC
- n(4)-acetylcytidine-5'-monophosphate
identifiers:
- ns: rnamods
id: '24'
- ns: pdb-ccd
id: 4AC
- ns: modomics.short_name
id: ac4C
- ns: modomics.new_nomenclature
id: 42C
- ns: cas
id: 3768-18-1
structure: CC(=O)Nc1ccn(c(=O)n1)[C@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 22
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
4C:
id: 4C
name: N4-methylcytidine
comments: <p>The base (m4Cyt) was previously reported in acid-treated HeLa rRNA,
and was presumed to have originated from N4,2'-O-dimethylcytidine.</p> <p>Phylogenetic
distribution<ul><li>eukarya rRNA</li></ul></p>
synonyms:
- m4C
- ν
identifiers:
- ns: modomics.new_nomenclature
id: 4C
- ns: modomics.short_name
id: m4C
- ns: cas
id: 10578-79-7
- ns: rnamods
id: '82'
structure: CNc1ccn(c(=O)n1)C1OC(C(C1O)O)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 16
l_bond_atoms:
- molecule: Monomer
element: P
position: 19
r_displaced_atoms:
- molecule: Monomer
element: H
position: 16
l_displaced_atoms:
- molecule: Monomer
element: O
position: 22
charge: -1
06A:
id: 06A
name: N6,2′-O-dimethyladenosine
comments: <p></p> <p>Phylogenetic distribution<ul><li>eukarya mRNA</li><li>eukarya
snRNA</li></ul></p>
synonyms:
- m6Am
- N6,2'-O-dimethyladenosine
- χ
identifiers:
- ns: modomics.short_name
id: m6Am
- ns: rnamods
id: '88'
- ns: modomics.new_nomenclature
id: 06A
- ns: cas
id: 57817-83-1
structure: COC1C(O)C(OC1n1cnc2c1ncnc2NC)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 22
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
066A:
id: 066A
name: N6,N6,2′-O-trimethyladenosine
comments: <p>Presence of m62Am in adenovirus mRNA was inferred from 3H labeling
data, but it was not chemically characterized.</p> <p>Phylogenetic distribution<ul><li>eukarya
mRNA</li></ul></p>
synonyms:
- N6,N6,2'-O-trimethyladenosine
- η
- m62Am
identifiers:
- ns: modomics.new_nomenclature
id: 066A
- ns: rnamods
id: '89'
- ns: modomics.short_name
id: m6,6Am
- ns: cas
id: 30891-53-3
structure: COC1C(O)C(OC1n1cnc2c1ncnc2N(C)C)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
66A:
id: 66A
name: N6,N6-dimethyladenosine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea rRNA</li><li>bacteria
rRNA</li><li>eukarya rRNA</li></ul></p>
synonyms:
- A
- '[(2R,3S,4R,5R)-5-(6-dimethylaminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- ζ
- MA6
- m62A
- 6n-dimethyladenosine-5'-monophoshate
- N,N-dimethyladenosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pubchem.compound
id: '72266'
- ns: rnamods
id: '80'
- ns: modomics.short_name
id: m6,6A
- ns: pdb-ccd
id: MA6
- ns: modomics.new_nomenclature
id: 66A
- ns: cas
id: 2620-62-4
structure: O[C@H]1[C@@H](O)[C@H](O[C@H]1n1cnc2c1ncnc2N(C)C)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
60A:
id: 60A
name: N6-(cis-hydroxyisopentenyl)adenosine
comments: <p>Also known as cis-zeatin riboside (symbol cZ). The name zeatin riboside
refers to the trans-isomer, a cytokinin (registry number 6025-53-2).</p> <p>Phylogenetic
distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- io6A
- '`'
identifiers:
- ns: cas
id: 15896-46-5
- ns: modomics.new_nomenclature
id: 60A
- ns: rnamods
id: '8'
- ns: modomics.short_name
id: io6A
structure: OCC(=CCNc1ncnc2c1ncn2C1OC(C(C1O)O)COP(=O)([O-])[O-])C
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 22
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
64A:
id: 64A
name: N6-acetyladenosine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li></ul></p>
synonyms:
- ac6A
- ⇓
identifiers:
- ns: rnamods
id: '102'
- ns: modomics.short_name
id: ac6A
- ns: cas
id: 16265-37-5
- ns: modomics.new_nomenclature
id: 64A
structure: CC(=O)Nc1ncnc2c1ncn2C1OC(C(C1O)O)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 20
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 20
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
67A:
id: 67A
name: N6-formyladenosine
synonyms:
- Ϩ
identifiers:
- ns: modomics.short_name
id: f6A
- ns: modomics.new_nomenclature
id: 67A
structure: O=CNc1ncnc2c1ncn2[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 22
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
65A:
id: 65A
name: N6-glycinylcarbamoyladenosine
comments: <p></p> <p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- g6A
- ≡
identifiers:
- ns: modomics.new_nomenclature
id: 65A
- ns: modomics.short_name
id: g6A
- ns: rnamods
id: '10'
- ns: cas
id: 29902-55-4
structure: O=C(Nc1ncnc2c1ncn2[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-])NCC(=O)[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 22
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
68A:
id: 68A
name: N6-hydroxymethyladenosine
synonyms:
- Ϫ
identifiers:
- ns: modomics.short_name
id: hm6A
- ns: modomics.new_nomenclature
id: 68A
structure: OCNc1ncnc2c1ncn2[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 22
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
63A:
id: 63A
name: N6-hydroxynorvalylcarbamoyladenosine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria
tRNA</li></ul></p>
synonyms:
- √
- hn6A
identifiers:
- ns: cas
id: 146426-20-2
- ns: modomics.short_name
id: hn6A
- ns: rnamods
id: '14'
- ns: modomics.new_nomenclature
id: 63A
structure: CCC(C(C(=O)[O-])NC(=O)Nc1ncnc2c1ncn2C1OC(C(C1O)O)COP(=O)([O-])[O-])O
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 27
l_bond_atoms:
- molecule: Monomer
element: P
position: 30
r_displaced_atoms:
- molecule: Monomer
element: H
position: 27
l_displaced_atoms:
- molecule: Monomer
element: O
position: 33
charge: -1
61A:
id: 61A
name: N6-isopentenyladenosine
comments: <p>i6A is somewhat characteristically eukaryal but does occur in some
bacterial tRNAs, e.g., E. coli. It appears to be absent in archaea. Symbol used
in early literature is IPA.</p> <p>Phylogenetic distribution<ul><li>bacteria
tRNA</li><li>eukarya tRNA</li></ul></p>
synonyms:
- +
- i6A
identifiers:
- ns: cas
id: 7724-76-7
- ns: pubchem.compound
id: '266767'
- ns: modomics.new_nomenclature
id: 61A
- ns: modomics.short_name
id: i6A
- ns: rnamods
id: '6'
structure: CC(=CCNc1ncnc2c1ncn2C1OC(C(C1O)O)COP(=O)([O-])[O-])C
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 21
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 21
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
662A:
id: 662A
name: N6-methyl-N6-threonylcarbamoyladenosine
comments: <p>Previously used symbol is mt6A.</p> <p>Phylogenetic distribution<ul><li>bacteria
tRNA</li></ul></p>
synonyms:
- A
- (2S,3R)-2-[[[9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]-methyl-carbamoyl]amino]-3-hydroxy-butanoic
acid
- E
- AET
- n-[n-(9-b-d-ribofuranosylpurin-6-yl)methylcarbamoyl]threonine-5'-monophosphate
- (2S,3R)-2-{[(9-{(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-9H-purin-6-yl)(methyl)carbamoyl]amino}-3-hydroxybutanoic
acid (non-preferred name)
- m6t6A
identifiers:
- ns: modomics.new_nomenclature
id: 662A
- ns: rnamods
id: '13'
- ns: pdb-ccd
id: AET
- ns: cas
id: 39667-81-7
- ns: modomics.short_name
id: m6t6A
structure: C[C@@H]([C@H](C(=O)O)NC(=O)N(c1ncnc2c1ncn2[C@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)([O-])[O-])C)O
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 32
l_bond_atoms:
- molecule: Monomer
element: P
position: 35
r_displaced_atoms:
- molecule: Monomer
element: H
position: 32
l_displaced_atoms:
- molecule: Monomer
element: O
position: 38
charge: -1
6A:
id: 6A
name: N6-methyladenosine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria
tRNA</li><li>archaea rRNA</li><li>bacteria rRNA</li><li>eukarya rRNA</li><li>eukarya
mRNA</li><li>eukarya snRNA</li></ul></p>
synonyms:
- m6A
- '='
identifiers:
- ns: cas
id: 1867-73-8
- ns: rnamods
id: '3'
- ns: modomics.short_name
id: m6A
- ns: modomics.new_nomenclature
id: 6A
structure: CNc1ncnc2c1ncn2C1OC(C(C1O)O)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 18
l_bond_atoms:
- molecule: Monomer
element: P
position: 21
r_displaced_atoms:
- molecule: Monomer
element: H
position: 18
l_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
62A:
id: 62A
name: N6-threonylcarbamoyladenosine
comments: <p>[1] reports characterization of the base of this nucleoside. The
L configuration for threonine in t6A was established in.</p> <p>Phylogenetic
distribution<ul><li>archaea tRNA</li><li>bacteria tRNA</li><li>eukarya tRNA</li></ul></p>
synonyms:
- t6A
- '6'
identifiers:
- ns: cas
id: 24719-82-2
- ns: rnamods
id: '11'
- ns: modomics.short_name
id: t6A
- ns: modomics.new_nomenclature
id: 62A
structure: O=C(Nc1ncnc2c1ncn2[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-])NC(=O)C(C(O)C)N
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 22
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
A:
id: A
name: adenosine
synonyms:
- A
- '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen
phosphate'
- adenosine-5'-monophosphate
- 5'-adenylic acid
identifiers:
- ns: pubchem.compound
id: '60961'
- ns: pdb-ccd
id: A
- ns: modomics.short_name
id: A
- ns: modomics.new_nomenclature
id: A
structure: OC1C(O)C(OC1n1cnc2c1ncnc2N)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 20
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
20C:
id: 20C
name: agmatidine
comments: <p>[1]</p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li></ul></p>
synonyms:
- C+
- ¿
identifiers:
- ns: rnamods
id: '113'
- ns: modomics.new_nomenclature
id: 20C
- ns: modomics.short_name
id: C+
- ns: cas
id: 1221169-70-5
structure: OC1C(O)C(OC1n1ccc(=N)[nH+]c1NCCCCNC(=[NH2+])N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 29
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 32
charge: -1
103G:
id: 103G
name: archaeosine
comments: "<p>Symbol G+ was assigned based on the positive charge carried by the\
\ nucleoside, as noted at the time of its original discovery; G* or G*-15 have\
\ been used but are no longer preferred. Alternate name is 7-formamidino-7-deazaguanosine.\
\ The Chemical Abstracts Index Name is based on nomenclature for the 4(1H)-quinazolinone\
\ ring system. Chemical synthesis of the corresponding base is reported in.\r\
\nThe bacterial nucleoside preQ0 is a biosynthetic precursor of G+.</p> <p>Phylogenetic\
\ distribution<ul><li>archaea tRNA</li></ul></p>"
synonyms:
- (
- G+
identifiers:
- ns: cas
id: 148608-52-0
- ns: modomics.short_name
id: G+
- ns: rnamods
id: '49'
- ns: modomics.new_nomenclature
id: 103G
structure: OC1[C@@H](O)[C@H](O[C@H]1n1cc(c2c1nc(N)[nH]c2=O)C(=[NH2+])N)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 30
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 33
charge: -1
69A:
id: 69A
name: cyclic N6-threonylcarbamoyladenosine
synonyms:
- e
identifiers:
- ns: modomics.new_nomenclature
id: 69A
- ns: modomics.short_name
id: ct6A
structure: OC1[C@@H](O)[C@H](O[C@H]1n1cnc2c1ncnc2/N=C\1/OC(=O)C(N1)C(O)C)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 32
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 35
charge: -1
C:
id: C
name: cytidine
synonyms:
- C
- 5'-cytidylic acid
- cytidine-5'-monophosphate
- '[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pubchem.compound
id: '6175'
- ns: modomics.short_name
id: C
- ns: pdb-ccd
id: C
- ns: modomics.new_nomenclature
id: C
structure: OC1C(O)C(OC1n1ccc(nc1=O)N)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 18
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 21
charge: -1
8U:
id: 8U
name: dihydrouridine
comments: <p></p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria
tRNA</li><li>eukarya tRNA</li><li>bacteria rRNA</li><li>eukarya snRNA</li><li>eukarya
chromosomal RNA</li></ul></p>
synonyms:
- 5'-uridylic acid
- '[(2R,3S,4R,5R)-5-(2,4-dioxo-1,3-diazinan-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- U
- H2U
- D
- 5,6-dihydrouridine-5'-monophosphate
identifiers:
- ns: rnamods
id: '51'
- ns: pubchem.compound
id: '94312'
- ns: cas
id: 5627-05-4
- ns: modomics.short_name
id: D
- ns: pdb-ccd
id: H2U
- ns: modomics.new_nomenclature
id: 8U
structure: O=C1CCN(C(=O)N1)[C@H]1O[C@@H]([C@H]([C@@H]1O)O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 19
l_bond_atoms:
- molecule: Monomer
element: P
position: 22
r_displaced_atoms:
- molecule: Monomer
element: H
position: 19
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
102G:
id: 102G
name: epoxyqueuosine
comments: <p></p> <p>Phylogenetic distribution<ul><li>bacteria tRNA</li></ul></p>
synonyms:
- oQ
- ς
identifiers:
- ns: modomics.short_name
id: oQtRNA
- ns: rnamods
id: '44'
- ns: cas
id: 107865-20-3
- ns: modomics.new_nomenclature
id: 102G
structure: OC1[C@@H](O)[C@H](O[C@H]1n1cc(c2c1nc(N)[nH]c2=O)CNC1C(O)C(C2C1O2)O)COP(=O)([O-])[O-]
base_monomers:
- 10G
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 35
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 38
charge: -1
104G:
id: 104G
name: galactosyl-queuosine
comments: <p>Symbol Q* is also used for either manQ, galQ, or a mixture of the
two.</p> <p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- galQ
- '9'
identifiers:
- ns: cas
id: 60426-58-6
- ns: modomics.new_nomenclature
id: 104G
- ns: rnamods
id: '45'
- ns: modomics.short_name
id: galQtRNA
structure: OCC1O[C@@H](OC2C(C=CC2O)NCc2cn(c3c2c(=O)[nH]c(n3)N)[C@@H]2O[C@@H](C([C@@H]2O)O)COP(=O)([O-])[O-])C([C@@H]([C@H]1O)O)O
base_monomers:
- 10G
r_bond_atoms:
- molecule: Monomer
element: O
position: 37
l_bond_atoms:
- molecule: Monomer
element: P
position: 40
r_displaced_atoms:
- molecule: Monomer
element: H
position: 37
l_displaced_atoms:
- molecule: Monomer
element: O
position: 43
charge: -1
G:
id: G
name: guanosine
synonyms:
- 5'-guanylic acid
- G
- guanosine-5'-monophosphate
- '[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: modomics.new_nomenclature
id: G
- ns: pdb-ccd
id: G
- ns: pubchem.compound
id: '6802'
- ns: modomics.short_name
id: G
structure: OC1C(O)C(OC1n1cnc2c1nc(N)[nH]c2=O)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 22
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
2165A:
id: 2165A
name: hydroxy-N6-threonylcarbamoyladenosine
synonyms:
- «
identifiers:
- ns: modomics.new_nomenclature
id: 2165A
- ns: modomics.short_name
id: ht6A
structure: OCC(C(C(=O)[O-])NC(=O)Nc1ncnc2c1ncn2[C@@H]1O[C@@H](C(C1O)O)COP(=O)([O-])[O-])O
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 29
l_bond_atoms:
- molecule: Monomer
element: P
position: 32
r_displaced_atoms:
- molecule: Monomer
element: H
position: 29
l_displaced_atoms:
- molecule: Monomer
element: O
position: 35
charge: -1
34830G:
id: 34830G
name: hydroxywybutosine
comments: <p>Nomenclature for the yW family of nucleosides is discussed in and.
Structural characterization was made from the acid-liberated base. A Chemical
Abstracts registry number was then assigned to the corresponding ribonucleoside.
Common name for the corresponding base is hydroxy-Y.</p> <p>Phylogenetic distribution<ul><li>eukarya
tRNA</li></ul></p>
synonyms:
- ⊆
- OHyW
identifiers:
- ns: rnamods
id: '39'
- ns: cas
id: 84270-21-3
- ns: modomics.new_nomenclature
id: 34830G
- ns: modomics.short_name
id: OHyW
structure: COC(=O)C(C(Cc1c(C)nc2n1c(=O)c1c(n2C)n(cn1)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-])O)NC(=O)OC
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 32
l_bond_atoms:
- molecule: Monomer
element: P
position: 35
r_displaced_atoms:
- molecule: Monomer
element: H
position: 32
l_displaced_atoms:
- molecule: Monomer
element: O
position: 38
charge: -1
9A:
id: 9A
name: inosine
comments: <p>The presence of I in mRNA had been implied earlier from discrepencies
between genomic and cDNA sequences, but provides the first direct evidence for
its occurrence.</p> <p>Phylogenetic distribution<ul><li>archaea tRNA</li><li>bacteria
tRNA</li><li>eukarya tRNA</li><li>eukarya mRNA</li></ul></p>
synonyms:
- 9-(5-O-phosphono-alpha-D-xylofuranosyl)-1,9-dihydro-6H-purin-6-one
- I
- '[(2R,3S,4R,5R)-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1H-purin-9-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- inosinic acid
identifiers:
- ns: pdb-ccd
id: I
- ns: rnamods
id: '17'
- ns: pubchem.compound
id: '6021'
- ns: cas
id: 58-63-9
- ns: modomics.short_name
id: I
- ns: modomics.new_nomenclature
id: 9A
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cnc2c1nc[nH]c2=O)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
42G:
id: 42G
name: isowyosine
comments: <p>Nomenclature for the yW family of nucleosides is discussed in and.
Numbering is based on 1H-imidazo[1,2-a]purine.</p> <p>Phylogenetic distribution<ul><li>archaea
tRNA</li></ul></p>
synonyms:
- imG2
- ⊇
identifiers:
- ns: cas
id: 577773-09-2
- ns: modomics.new_nomenclature
id: 42G
- ns: modomics.short_name
id: imG2
- ns: rnamods
id: '101'
structure: OC1C(COP(=O)([O-])[O-])OC(C1O)n1cnc2c1[nH]c1nc(c(n1c2=O)C)C
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
l_bond_atoms:
- molecule: Monomer
element: P
position: 6
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
106G:
id: 106G
name: mannosyl-queuosine
synonyms:
- '8'
identifiers:
- ns: modomics.short_name
id: manQtRNA
- ns: modomics.new_nomenclature
id: 106G
structure: OCC1O[C@@H](OC2C(C=CC2O)NCc2cn(c3c2c(=O)[nH]c(n3)N)[C@@H]2O[C@@H](C([C@@H]2O)O)COP(=O)([O-])[O-])C([C@@H]([C@@H]1O)O)O
base_monomers:
- 10G
r_bond_atoms:
- molecule: Monomer
element: O
position: 37
l_bond_atoms:
- molecule: Monomer
element: P
position: 40
r_displaced_atoms:
- molecule: Monomer
element: H
position: 37
l_displaced_atoms:
- molecule: Monomer
element: O
position: 43
charge: -1
3480G:
id: 3480G
name: methylated undermodified hydroxywybutosine
synonyms:
- y
identifiers:
- ns: modomics.new_nomenclature
id: 3480G
- ns: modomics.short_name
id: OHyWy
structure: COC(=O)C(C(Cc1c(C)nc2n1c(=O)c1c(n2C)n(cn1)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-])O)N
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 32
l_bond_atoms:
- molecule: Monomer
element: P
position: 35
r_displaced_atoms:
- molecule: Monomer
element: H
position: 32
l_displaced_atoms:
- molecule: Monomer
element: O
position: 38
charge: -1
342G:
id: 342G
name: methylwyosine
comments: <p>Nomenclature for the yW family of nucleosides is discussed in and.</p>
<p>Phylogenetic distribution<ul><li>archaea tRNA</li></ul></p>
synonyms:
- mimG
- ∑
identifiers:
- ns: modomics.new_nomenclature
id: 342G
- ns: cas
id: 108274-04-0
- ns: modomics.short_name
id: mimG
- ns: rnamods
id: '42'
structure: OC1C(COP(=O)([O-])[O-])OC(C1O)n1cnc2c1n(C)c1nc(c(n1c2=O)C)C
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
l_bond_atoms:
- molecule: Monomer
element: P
position: 6
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: O
position: 9
charge: -1
34832G:
id: 34832G
name: peroxywybutosine
comments: <p>Nomenclature for the yW family of nucleosides is discussed in and.
Structural characterization was made from the acid-liberated base. A Chemical
Abstracts registry number was then assigned to the corresponding ribonucleoside.
Alternate name is wybutoxine. Common name for the corresponding base is peroxy-Y,
symbol Yr. Initial report in with complete characterization in. Occurrence of
the peroxy function in the natural nucleoside has been questioned and led to
the confusing use of Yr as a symbol for the base of hydroxywybutosine in.</p>
<p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- W
- o2yW
identifiers:
- ns: modomics.short_name
id: o2yW
- ns: cas
id: 78355-49-4
- ns: modomics.new_nomenclature
id: 34832G
- ns: rnamods
id: '38'
structure: OOC(C(C(=O)OC)NC(=O)OC)Cc1c(C)nc2n1c(=O)c1c(n2C)n(cn1)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 39
l_bond_atoms:
- molecule: Monomer
element: P
position: 42
r_displaced_atoms:
- molecule: Monomer
element: H
position: 39
l_displaced_atoms:
- molecule: Monomer
element: O
position: 45
charge: -1
9U:
id: 9U
name: pseudouridine
comments: <p>The structure of pseudouridine was determined by Yu and Allen from
material isolated from unfractionated yeast RNA, and was independently reported
by Cohn in a manuscript submitted eight days later. Leading references to the
pseudouridine literature can be found in a recent review.</p> <p>Phylogenetic
distribution<ul><li>archaea tRNA</li><li>bacteria tRNA</li><li>eukarya tRNA</li><li>archaea
rRNA</li><li>bacteria rRNA</li><li>eukarya rRNA</li><li>bacteria tmRNA</li><li>eukarya
snRNA</li></ul></p>
synonyms:
- '[(2R,3S,4R,5S)-5-(2,4-dioxo-1H-pyrimidin-5-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- PSU
- pseudouridine-5'-monophosphate
- (1S)-1,4-anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitol
- U
- P
- Y
identifiers:
- ns: pubchem.compound
id: '15047'
- ns: modomics.short_name
id: Y
- ns: rnamods
id: '50'
- ns: cas
id: 1445-07-4
- ns: modomics.new_nomenclature
id: 9U
- ns: pdb-ccd
id: PSU
structure: O[C@H]1[C@H](O)[C@@H](O[C@H]1c1c[nH]c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
10G:
id: 10G
name: queuosine
comments: <p>Characterization of queuine, the base of queuosine, is reported in.
Biosynthesis of qeuosine has recently been reviewed.</p> <p>Phylogenetic distribution<ul><li>bacteria
tRNA</li><li>eukarya tRNA</li></ul></p>
synonyms:
- Q
identifiers:
- ns: cas
id: 57072-36-3
- ns: modomics.short_name
id: QtRNA
- ns: rnamods
id: '43'
- ns: modomics.new_nomenclature
id: 10G
structure: OC1[C@@H](O)[C@H](O[C@H]1n1cc(c2c1nc(N)[nH]c2=O)CNC1C=CC(C1O)O)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 5
l_bond_atoms:
- molecule: Monomer
element: P
position: 34
r_displaced_atoms:
- molecule: Monomer
element: H
position: 5
l_displaced_atoms:
- molecule: Monomer
element: O
position: 37
charge: -1
3470G:
id: 3470G
name: undermodified hydroxywybutosine
synonyms:
- š
identifiers:
- ns: modomics.new_nomenclature
id: 3470G
- ns: modomics.short_name
id: OHyWx
structure: OC(C(C(=O)[O-])[NH3+])Cc1c(C)nc2n1c(=O)c1c(n2C)n(cn1)[C@@H]1O[C@@H]([C@@H](C1O)O)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 36
l_bond_atoms:
- molecule: Monomer
element: P
position: 39
r_displaced_atoms:
- molecule: Monomer
element: H
position: 36
l_displaced_atoms:
- molecule: Monomer
element: O
position: 42
charge: -1
U:
id: U
name: uridine
synonyms:
- '[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- 5'-uridylic acid
- uridine-5'-monophosphate
- U
identifiers:
- ns: modomics.short_name
id: U
- ns: pdb-ccd
id: U
- ns: modomics.new_nomenclature
id: U
- ns: pubchem.compound
id: '6029'
structure: OC1C(O)C(OC1n1ccc(=O)[nH]c1=O)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 4
l_bond_atoms:
- molecule: Monomer
element: P
position: 19
r_displaced_atoms:
- molecule: Monomer
element: H
position: 4
l_displaced_atoms:
- molecule: Monomer
element: O
position: 22
charge: -1
502U:
id: 502U
name: uridine 5-oxyacetic acid
comments: <p>Alternate commonly used symbols are o5U and V.</p> <p>Phylogenetic
distribution<ul><li>bacteria tRNA</li></ul></p>
synonyms:
- cmo5U
- V
identifiers:
- ns: modomics.short_name
id: cmo5U
- ns: cas
id: 28144-25-4
- ns: modomics.new_nomenclature
id: 502U
- ns: pubchem.compound
id: '193091'
- ns: rnamods
id: '64'
structure: '[O-]C(=O)COc1cn(c(=O)[nH]c1=O)C1OC(C(C1O)O)COP(=O)([O-])[O-]'
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 21
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 21
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
503U:
id: 503U
name: uridine 5-oxyacetic acid methyl ester
comments: <p>Alternate commonly used symbol is mV.</p> <p>Phylogenetic distribution<ul><li>bacteria
tRNA</li></ul></p>
synonyms:
- υ
- mcmo5U
identifiers:
- ns: cas
id: 66536-81-0
- ns: modomics.new_nomenclature
id: 503U
- ns: pubchem.compound
id: '191808'
- ns: rnamods
id: '65'
- ns: modomics.short_name
id: mcmo5U
structure: COC(=O)COc1cn(c(=O)[nH]c1=O)C1OC(C(C1O)O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 22
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
3483G:
id: 3483G
name: wybutosine
comments: <p>Nomenclature for the yW family of nucleosides is discussed in and.
Errata for structure determination of yW are reported in. Alternate commonly
used name is "Y nucleoside". Commonly used symbol for the corresponding base
is Y. Structural characterization was made from the acid-liberated base. A Chemical
Abstracts registry number was then assigned to the corresponding ribonucleoside.</p>
<p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
synonyms:
- G
- YYG
- yW
- 4-(3-[5-o-phosphonoribofuranosyl]-4,6-dimethyl-8-oxo-4,8-dihydro-3h-1,3,4,5,7a-pentaaza-s-indacen-ylamino-butyric
acid methyl ester
- methyl (2S)-4-[3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-4,6-dimethyl-9-oxo-imidazo[3,2-a]purin-7-yl]-2-(methoxycarbonylamino)butanoate
- Y
- 7-{(3S)-4-methoxy-3-[(methoxycarbonyl)amino]-4-oxobutyl}-4,6-dimethyl-3-(5-O-phosphono-beta-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
identifiers:
- ns: pdb-ccd
id: YYG
- ns: cas
id: 55196-46-8
- ns: modomics.new_nomenclature
id: 3483G
- ns: rnamods
id: '37'
- ns: modomics.short_name
id: yW
structure: COC(=O)[C@@H](NC(=O)OC)CCc1c(C)nc2n1c(=O)c1c(n2C)n(cn1)[C@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 39
l_bond_atoms:
- molecule: Monomer
element: P
position: 42
r_displaced_atoms:
- molecule: Monomer
element: H
position: 39
l_displaced_atoms:
- molecule: Monomer
element: O
position: 45
charge: -1
34G:
id: 34G
name: wyosine
comments: <p>Nomenclature for the yW family of nucleosides is discussed in and.
Structural characterization was made from the acid-liberated base. A Chemical
Abstracts registry number was then assigned to the corresponding ribonucleoside.
Symbol for the corresponding base is Yt.</p> <p>Phylogenetic distribution<ul><li>archaea
tRNA</li><li>eukarya tRNA</li></ul></p>
synonyms:
- €
- imG
identifiers:
- ns: cas
id: 52662-10-9
- ns: modomics.new_nomenclature
id: 34G
- ns: rnamods
id: '41'
- ns: modomics.short_name
id: imG
structure: O[C@@H]1[C@H](O)[C@H](O[C@H]1n1cnc2c1n(C)c1n(c2=O)cc(n1)C)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 29
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 32
charge: -1
OHyW*:
id: OHyW*
name: undermodified hydroxywybutosine
comments: <p>Nomenclature for the yW nucleosides is discussed in and. Structure
characterization was from the acid-liberated base. A Chemical Abstracts registry
number was then assigned to the corresponding ribonucleoside. Symbol for the
corresponding base is Ye.</p> <p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
identifiers:
- ns: cas
id: 84270-20-2
- ns: rnamods
id: '40'
structure: OC(C(C(=O)[O-])[NH3+])Cc1c(C)nc2n1c(=O)c1c(n2C)ncn1[C@@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 37
l_bond_atoms:
- molecule: Monomer
element: P
position: 40
r_displaced_atoms:
- molecule: Monomer
element: H
position: 37
l_displaced_atoms:
- molecule: Monomer
element: O
position: 43
charge: -1
manQ:
id: manQ
name: mannosyl-queuosine
comments: <p>Symbol Q* is also used for either manQ, galQ, or a mixture of the
two.</p> <p>Phylogenetic distribution<ul><li>eukarya tRNA</li></ul></p>
identifiers:
- ns: rnamods
id: '46'
- ns: cas
id: 60398-20-1
structure: OC[C@H]1O[C@@H](O[C@@H]2[C@H](C=C[C@@H]2O)NCc2cn(c3c2c(=O)nc([nH]3)N)[C@@H]2O[C@@H]([C@H]([C@H]2O)O)COP(=O)([O-])[O-])[C@H]([C@H]([C@@H]1O)O)O
base_monomers:
- 10G
r_bond_atoms:
- molecule: Monomer
element: O
position: 42
l_bond_atoms:
- molecule: Monomer
element: P
position: 45
r_displaced_atoms:
- molecule: Monomer
element: H
position: 42
l_displaced_atoms:
- molecule: Monomer
element: O
position: 48
charge: -1
10C:
id: 10C
name: 4-amino-1-{2,5-anhydro-4-[(phosphonooxy)methyl]-alpha-l-lyxofuranosyl}pyrimidin-2(1h)-one
synonyms:
- C
- 4-amino-1-{2,5-anhydro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}pyrimidin-2(1H)-one
- '[(1R,4R,5R,7S)-5-(4-amino-2-oxo-pyrimidin-1-yl)-7-hydroxy-3,6-dioxabicyclo[2.2.1]heptan-1-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 10C
structure: Nc1ccn(c(=O)n1)[C@@H]1O[C@]2([C@H]([C@H]1OC2)O)COP(=O)(O)O
base_monomers:
- C
'125':
id: '125'
name: 2'-o-fluoroethyl-5-methyl-uridine-5'-monophosphate
synonyms:
- '[(2R,3R,4R,5R)-4-(2-fluoroethoxy)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- 2'-O-(2-fluoroethyl)-5-methyluridine 5'-(dihydrogen phosphate)
- U
identifiers:
- ns: pdb-ccd
id: '125'
structure: FCCO[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 9
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
'126':
id: '126'
name: 2'-o-methyl-[tri(oxyethyl)]-5-methyl-uridine-5'-monophosphate
synonyms:
- '[(2R,3R,4R,5R)-3-hydroxy-4-[2-[2-(2-methoxyethoxy)ethoxy]ethoxy]-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- 2'-O-{2-[2-(2-methoxyethoxy)ethoxy]ethyl}-5-methyluridine 5'-(dihydrogen phosphate)
- U
identifiers:
- ns: pdb-ccd
id: '126'
structure: COCCOCCOCCO[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 16
l_bond_atoms:
- molecule: Monomer
element: P
position: 34
r_displaced_atoms:
- molecule: Monomer
element: H
position: 16
l_displaced_atoms:
- molecule: Monomer
element: O
position: 37
charge: -1
'127':
id: '127'
name: 2'-o-aminooxy-ethyl-5-methyl-uridine-5'-monophosphate
synonyms:
- '[(2R,3R,4R,5R)-4-(2-aminooxyethoxy)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- 2'-O-[2-(aminooxy)ethyl]-5-methyluridine 5'-(dihydrogen phosphate)
- U
identifiers:
- ns: pdb-ccd
id: '127'
structure: NOCCO[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 10
l_bond_atoms:
- molecule: Monomer
element: P
position: 28
r_displaced_atoms:
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: O
position: 31
charge: -1
18M:
id: 18M
name: 2'-o-methylguanosine 3',5'-bis(dihydrogen phosphate)
synonyms:
- '[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-4-methoxy-2-(phosphonooxymethyl)oxolan-3-yl]
dihydrogen phosphate'
- 2'-O-methylguanosine 3',5'-bis(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 18M
structure: CO[C@@H]1[C@@H](OP(=O)(O)O)[C@@H](O[C@@H]1n1cnc2c1[nH]c(N)nc2=O)COP(=O)([O-])[O-]
base_monomers:
- G
l_bond_atoms:
- molecule: Monomer
element: P
position: 31
l_displaced_atoms:
- molecule: Monomer
element: O
position: 33
charge: -1
1DP:
id: 1DP
name: n1-deaza-adenosine-5'-monophosphate
synonyms:
- 3-(5-O-phosphono-beta-D-ribofuranosyl)-3H-imidazo[4,5-b]pyridin-7-amine
- '[(2R,3S,4R,5R)-5-(7-aminoimidazo[5,4-b]pyridin-3-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 1DP
structure: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1n1cnc2c1nccc2N)COP(=O)(O)O
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
1PR:
id: 1PR
name: phosphoric acid mono-[5-({[5-carbamoyl-3-(5-phosphonooxy-5-deoxy-ribofuranosyl)-
3h-imidazol-4-ylamino]-methyl}-amino)-2,3,4-trihydroxy-pentyl] ester
synonyms:
- '[(2R,3S)-5-[[[5-aminocarbonyl-3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]imidazol-4-yl]amino]methylamino]-2,3,4-trihydroxy-pentyl]
dihydrogen phosphate'
- N
identifiers:
- ns: pdb-ccd
id: 1PR
structure: O[C@H]([C@@H](COP(=O)(O)O)O)[C@H](CNCNc1n(cnc1C(=O)N)[C@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)(O)O)O
r_bond_atoms:
- molecule: Monomer
element: O
position: 37
r_displaced_atoms:
- molecule: Monomer
element: H
position: 37
1RN:
id: 1RN
name: (e)-n-{[4-oxo-1-(5-o-phosphono-beta-d-arabinofuranosyl)-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl]methylidene}glycine
synonyms:
- (E)-N-{[4-oxo-1-(5-O-phosphono-beta-D-arabinofuranosyl)-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl]methylidene}glycine
- 2-[(E)-[1-[(2R,3S,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-4-oxidanylidene-2-sulfanylidene-pyrimidin-5-yl]methylideneamino]ethanoic
acid
identifiers:
- ns: pdb-ccd
id: 1RN
structure: OC(=O)C/N=C/c1cn(c(=S)[nH]c1=O)[C@@H]1O[C@H]([C@@H]([C@@H]1O)O)COP(=O)(O)O
base_monomers:
- U
1SC:
id: 1SC
name: 5'-o-thiophosphonocytidine
synonyms:
- C
- '[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-sulfanyl-phosphinic
acid'
- 5'-O-thiophosphonocytidine
identifiers:
- ns: pdb-ccd
id: 1SC
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1ccc(nc1=O)N)CO[P@@](=O)(S)O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
23G:
id: 23G
name: guanosine-5'-phosphate-2',3'-cyclic phosphate
synonyms:
- '[(2S,3aR,4R,6R,6aR)-6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-hydroxy-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]methyl
dihydrogen phosphate'
- '[(1R,3S,5R,6R,8R)-8-(2-azanyl-6-oxo-1H-purin-9-yl)-3-hydroxy-3-oxo-2,4,7-trioxa-3$l^{5}-phosphabicyclo[3.3.0]octan-6-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 23G
structure: Nc1[nH]c(=O)c2c(n1)n(cn2)[C@@H]1O[C@H]([C@H]2[C@@H]1O[P@@](=O)(O2)O)COP(=O)([O-])[O-]
base_monomers:
- G
l_bond_atoms:
- molecule: Monomer
element: P
position: 29
l_displaced_atoms:
- molecule: Monomer
element: O
position: 32
charge: -1
2AT:
id: 2AT
name: 2'-o-allyl thymidine-5'-monophosphate
synonyms:
- 5-methyl-2'-O-prop-2-en-1-yluridine 5'-(dihydrogen phosphate)
- T
- '[(2R,3R,4R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-4-prop-2-enoxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 2AT
structure: C=CCO[C@H]1[C@@H](O)[C@H](O[C@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 9
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
2AU:
id: 2AU
name: 2'-aminouridine
synonyms:
- '[(2R,3S,4R,5R)-4-amino-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- 2'-amino-2'-deoxyuridine 5'-(dihydrogen phosphate)
- U
identifiers:
- ns: pdb-ccd
id: 2AU
structure: N[C@H]1[C@H](O)[C@H](O[C@@H]1n1ccc(=O)[nH]c1=O)COP(=O)(O)O
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
2BT:
id: 2BT
name: 2'-o-butyl-thymidine
synonyms:
- '[(2R,3R,4R,5R)-4-butoxy-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- T
- 2'-O-butyl-5-methyluridine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 2BT
structure: CCCCO[C@H]1[C@@H](O)[C@H](O[C@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 10
l_bond_atoms:
- molecule: Monomer
element: P
position: 28
r_displaced_atoms:
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
2GT:
id: 2GT
name: 2'-o-propargyl thymidine-5'-monophosphate
synonyms:
- T
- '[(2R,3R,4R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-4-prop-2-ynoxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- 5-methyl-2'-O-prop-2-yn-1-yluridine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 2GT
structure: C#CCO[C@H]1[C@@H](O)[C@H](O[C@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 9
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
2MA:
id: 2MA
name: 2-methyladenosine-5'-monophosphate
synonyms:
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-(6-imino-2-methyl-1H-purin-9-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- A
- 2-methyladenosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 2MA
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cnc2c1nc(C)[nH]c2=N)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
2NT:
id: 2NT
name: 2'-o-[2-[hydroxy(methyleneamino)oxy]ethyl thymidine-5'-monophosphate
synonyms:
- 2'-O-(2-{[(hydroxymethyl)amino]oxy}ethyl)-5-methyluridine 5'-(dihydrogen phosphate)
- T
- '[(2R,3R,4R,5R)-3-hydroxy-4-[2-(hydroxymethylamino)oxyethoxy]-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 2NT
structure: OCNOCCO[C@H]1[C@@H](O)[C@H](O[C@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 12
l_bond_atoms:
- molecule: Monomer
element: P
position: 30
r_displaced_atoms:
- molecule: Monomer
element: H
position: 12
l_displaced_atoms:
- molecule: Monomer
element: O
position: 32
charge: -1
2OM:
id: 2OM
name: 5,6-dihydroorotidine 5'-monophosphate
synonyms:
- (4R)-3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-2,6-dioxo-1,3-diazinane-4-carboxylic
acid
- 6-carboxyuridine 5'-(dihydrogen phosphate)
- U
identifiers:
- ns: pdb-ccd
id: 2OM
structure: O=C1NC(=O)N([C@@H](C1)C(=O)O)[C@H]1O[C@H]([C@H]([C@H]1O)O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 23
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
r_displaced_atoms:
- molecule: Monomer
element: H
position: 23
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
2OT:
id: 2OT
name: 2'-o-[2-(n,n-dimethylaminooxy)ethyl] thymidine-5'-monophosphate
synonyms:
- 2'-O-{2-[(dimethylamino)oxy]ethyl}-5-methyluridine 5'-(dihydrogen phosphate)
- T
- '[(2R,3R,4R,5R)-4-(2-dimethylaminooxyethoxy)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 2OT
structure: CN(OCCO[C@H]1[C@@H](O)[C@H](O[C@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-])C
r_bond_atoms:
- molecule: Monomer
element: O
position: 11
l_bond_atoms:
- molecule: Monomer
element: P
position: 29
r_displaced_atoms:
- molecule: Monomer
element: H
position: 11
l_displaced_atoms:
- molecule: Monomer
element: O
position: 32
charge: -1
2SA:
id: 2SA
name: 2-[9-(3,4-dihydroxy-5-phosphonooxymethyl-tetrahydro-furan-2-yl)-9h-purin-6-ylamino]-succinic
acid
synonyms:
- (2S)-2-[(9-{(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-9H-purin-6-yl)amino]butanedioic
acid (non-preferred name)
- (2S)-2-[[9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]amino]butanedioic
acid
- N
identifiers:
- ns: pdb-ccd
id: 2SA
structure: OC(=O)C[C@H](C(=O)O)Nc1ncnc2c1ncn2[C@@H]1O[C@@H]([C@@H]([C@@H]1O)O)COP(=O)(O)O
2SG:
id: 2SG
name: guanosine phosphorodithioate
synonyms:
- 2-azanyl-9-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-[[oxidanyl-bis(sulfanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]-1H-purin-6-one
- 5'-O-[hydroxy(disulfanyl)-lambda~5~-phosphanyl]guanosine
identifiers:
- ns: pdb-ccd
id: 2SG
structure: O[C@H]1[C@H](O)[C@H](O[C@H]1n1cnc2c1nc(N)[nH]c2=O)COP(S)(S)O
base_monomers:
- G
31H:
id: 31H
name: 3'-deoxy-3'-[(n-formyl-l-methionyl)amino]adenosine 5'-(dihydrogen phosphate)
synonyms:
- '[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3-[[(2S)-2-formamido-4-methylsulfanyl-butanoyl]amino]-4-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- 3'-deoxy-3'-[(N-formyl-L-methionyl)amino]adenosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 31H
structure: CSCC[C@H](C(=O)N[C@@H]1[C@H](COP(=O)([O-])[O-])O[C@H]([C@@H]1O)n1cnc2c1ncnc2N)NC=O
base_monomers:
- A
l_bond_atoms:
- molecule: Monomer
element: P
position: 16
l_displaced_atoms:
- molecule: Monomer
element: O
position: 19
charge: -1
31M:
id: 31M
name: 3'-deoxy-3'-[(l-methionyl-l-phenylalanyl)amino]adenosine 5'-(dihydrogen
phosphate)
synonyms:
- '[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3-[[(2S)-2-[[(2S)-2-azanyl-4-methylsulfanyl-butanoyl]amino]-3-phenyl-propanoyl]amino]-4-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- 3'-deoxy-3'-[(L-methionyl-L-phenylalanyl)amino]adenosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 31M
structure: CSCC[C@H](C(=O)N[C@H](C(=O)N[C@H]1[C@@H](COP(=O)([O-])[O-])O[C@H]([C@@H]1O)n1cnc2c1ncnc2N)Cc1ccccc1)N
base_monomers:
- A
l_bond_atoms:
- molecule: Monomer
element: P
position: 21
l_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
3AU:
id: 3AU
name: 3-[(3s)-3-amino-3-carboxypropyl]uridine 5'-(dihydrogen phosphate)
synonyms:
- (2S)-2-azanyl-4-[3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-2,6-dioxo-pyrimidin-1-yl]butanoic
acid
- 3-[(3S)-3-amino-3-carboxypropyl]uridine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 3AU
structure: OC(=O)[C@H](CCn1c(=O)ccn(c1=O)[C@@H]1O[C@H]([C@@H]([C@@H]1O)O)COP(=O)(O)O)N
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 26
r_displaced_atoms:
- molecule: Monomer
element: H
position: 26
3DA:
id: 3DA
name: 3'-deoxyadenosine-5'-monophosphate
synonyms:
- A
- '[(2S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate'
- 3'-deoxy-5'-adenylic acid
identifiers:
- ns: pdb-ccd
id: 3DA
structure: O[C@H]1C[C@H](O[C@H]1n1cnc2c1ncnc2N)COP(=O)(O)O
3ME:
id: 3ME
name: 2'-o-{2-[2-(dimethylamino)ethoxy]ethyl}-5-methyluridine 5'-(dihydrogen phosphate)
synonyms:
- 2'-O-{2-[2-(dimethylamino)ethoxy]ethyl}-5-methyluridine 5'-(dihydrogen phosphate)
- '[(2R,3R,4R,5R)-4-[2-(2-dimethylaminoethyloxy)ethoxy]-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- U
identifiers:
- ns: pdb-ccd
id: 3ME
structure: CN(CCOCCO[C@H]1[C@@H](O)[C@H](O[C@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)(O)O)C
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 13
r_displaced_atoms:
- molecule: Monomer
element: H
position: 13
3TD:
id: 3TD
name: (1s)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-o-phosphono-d-ribitol
synonyms:
- (1S)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitol
- '[(2R,3S,4R,5S)-5-[3-methyl-2,4-bis(oxidanylidene)-1H-pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 3TD
structure: O[C@H]1[C@@H](O)[C@@H](O[C@H]1c1c[nH]c(=O)n(c1=O)C)COP(=O)(O)O
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
45A:
id: 45A
name: 5'-o-[(s)-hydroxy(methyl)phosphoryl]adenosine
synonyms:
- A
- 5'-O-[(S)-hydroxy(methyl)phosphoryl]adenosine
- '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-methyl-phosphinic
acid'
identifiers:
- ns: pdb-ccd
id: 45A
structure: O[C@@H]1[C@@H](O)[C@@H](O[C@H]1n1cnc2c1ncnc2N)CO[P@](=O)(O)C
base_monomers:
- A
4TA:
id: 4TA
name: p1-(5'-adenosyl)p4-(5'-(2'-deoxy-thymidyl))tetraphosphate
synonyms:
- '[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-phosphoryl]
[[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanidyl-phosphoryl]oxy-oxidanidyl-phosphoryl]
phosphate'
- N
identifiers:
- ns: pdb-ccd
id: 4TA
structure: O[C@@H]1C[C@@H](O[C@@H]1CO[P@@](=O)(O[P@@](=O)(O[P@@](=O)(O[P@@](=O)(OC[C@H]1O[C@@H]([C@H]([C@H]1O)O)n1cnc2c1ncnc2N)[O-])[O-])[O-])[O-])n1cc(C)c(=O)[nH]c1=O
50L:
id: 50L
name: '[(2r,3s,4r,5r)-5-(4-azanyl-2-oxidanylidene-1$l^{4},3,5,7-tetrazabicyclo[4.3.0]nona-1(6),3,8-trien-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
synonyms:
- '[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-1$l^{4},3,5,7-tetrazabicyclo[4.3.0]nona-1(6),3,8-trien-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 50L
structure: NC1NC(=O)N2C(N1)N(CC2)[C@@H]1O[C@@H]([C@@H]([C@H]1O)O)COP(=O)(O)O
50N:
id: 50N
name: (1s)-1-(6-amino-2-hydroxy-5-nitropyridin-3-yl)-1,4-anhydro-5-o-phosphono-d-ribitol
synonyms:
- (1S)-1-(6-amino-2-hydroxy-5-nitropyridin-3-yl)-1,4-anhydro-5-O-phosphono-D-ribitol
- '[(2R,3S,4R,5S)-5-(6-azanyl-5-nitro-2-oxidanyl-pyridin-3-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 50N
structure: O[C@H]1[C@H](O)[C@H](O[C@H]1c1cc([N+](=O)[O-])c(nc1O)N)COP(=O)([O-])[O-]
56B:
id: 56B
name: 2-amino-5-({[(1s,4s,5r)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-o-phosphono-beta-d-ribofuranosyl)-3,7-dihydro-4h-pyrrolo[2,3-d]pyrimidin-4-one
synonyms:
- 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
- '[(2R,3S,4R,5R)-5-[2-azanyl-5-[[[(1S,4S,5R)-4,5-bis(oxidanyl)cyclopent-2-en-1-yl]amino]methyl]-4-oxidanylidene-3H-pyrrolo[2,3-d]pyrimidin-7-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 56B
structure: O[C@H]1[C@@H](O)[C@H](O[C@H]1n1cc(c2c1nc(N)[nH]c2=O)CN[C@H]1C=C[C@H]([C@@H]1O)O)CO[P@@](=O)(O)[O-]
'574':
id: '574'
name: '[(3as,4r,6r,6ar)-2-{2-[(1s)-2-amino-1-hydroxyethyl]phenyl}-6-(6-amino-9h-purin-9-yl)tetrahydrofuro[3,4-d][1,3,2]dioxaborol-4-yl]methyl
dihydrogen phosphite'
synonyms:
- '[(3aR,4R,6R,6aS)-4-(6-aminopurin-9-yl)-2-[2-[(1S)-2-azanyl-1-oxidanyl-ethyl]phenyl]-3a,4,6,6a-tetrahydrofuro[3,4-d][1,3,2]dioxaborol-6-yl]methyl
dihydrogen phosphate'
- '[(3aS,4R,6R,6aR)-2-{2-[(1S)-2-amino-1-hydroxyethyl]phenyl}-6-(6-amino-9H-purin-9-yl)tetrahydrofuro[3,4-d][1,3,2]dioxaborol-4-yl]methyl
dihydrogen phosphite'
identifiers:
- ns: pdb-ccd
id: '574'
structure: NC[C@H](c1ccccc1B1O[C@H]2[C@H](O1)[C@@H](O[C@@H]2n1cnc2c1ncnc2N)COP(=O)(O)O)O
5AA:
id: 5AA
name: n6-dimethyl-3'-amino-adenosine-5'-monophosphate
synonyms:
- A
- 3'-amino-3'-deoxy-N,N-dimethyladenosine 5'-(dihydrogen phosphate)
- '[(2S,3S,4R,5R)-3-amino-5-(6-dimethylaminopurin-9-yl)-4-hydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 5AA
structure: O[C@H]1[C@@H](N)[C@H](O[C@H]1n1cnc2c1ncnc2N(C)C)COP(=O)([O-])[O-]
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
5BU:
id: 5BU
name: 5-bromo-uridine-5'-monophosphate
synonyms:
- 5-bromouridine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-5-(5-bromo-2,4-dioxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- U
identifiers:
- ns: pdb-ccd
id: 5BU
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cc(Br)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
5CF:
id: 5CF
name: 5-fluorocytidine 5'-(dihydrogen phosphate)
synonyms:
- 5-fluorocytidine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-5-(4-azanyl-5-fluoro-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 5CF
structure: O[C@@H]1[C@@H](O)[C@H](O[C@H]1n1cc(F)c(nc1=O)N)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
5CG:
id: 5CG
name: 5'-chloro-5'-deoxy-guanosine
synonyms:
- 2-amino-9-[(2R,3R,4S,5S)-5-(chloromethyl)-3,4-dihydroxy-oxolan-2-yl]-1H-purin-6-one
- G
- 5'-chloro-5'-deoxyguanosine
identifiers:
- ns: pdb-ccd
id: 5CG
structure: ClC[C@H]1O[C@@H]([C@@H]([C@@H]1O)O)n1cnc2c1nc(N)[nH]c2=O
r_bond_atoms:
- molecule: Monomer
element: O
position: 12
r_displaced_atoms:
- molecule: Monomer
element: H
position: 12
5FA:
id: 5FA
name: adenosine-5'-pentaphosphate
synonyms:
- A
- 5'-O-[(S)-hydroxy{[(R)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]adenosine
- '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[hydroxy-(hydroxy-phosphonooxy-phosphoryl)oxy-phosphoryl]oxy-phosphoryl]
hydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 5FA
structure: O[C@@H]1[C@@H](CO[P@](=O)(O[P@](=O)(O[P@](=O)(O[P@](=O)(OP(=O)(O)O)O)O)O)O)O[C@@H]([C@@H]1O)n1cnc2c1ncnc2N
base_monomers:
- A
5FU:
id: 5FU
name: 5-fluoro-uridine-5'-monophosphate
synonyms:
- '[(2R,3S,4R,5R)-5-(5-fluoro-2,4-dioxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- 5-fluorouridine 5'-(dihydrogen phosphate)
- U
identifiers:
- ns: pdb-ccd
id: 5FU
structure: O[C@@H]1[C@@H](O)[C@@H](O[C@@H]1n1cc(F)c(=O)[nH]c1=O)COP(=O)(O)O
base_monomers:
- U
5HM:
id: 5HM
name: 5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)
synonyms:
- 5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-5-[4-azanyl-5-(hydroxymethyl)-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 5HM
structure: OCc1cn(c(=O)nc1N)[C@H]1O[C@H]([C@H]([C@@H]1O)O)COP(=O)(O)O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 21
r_displaced_atoms:
- molecule: Monomer
element: H
position: 21
5IC:
id: 5IC
name: 5-iodo-cytidine-5'-monophosphate
synonyms:
- C
- 4-amino-5-iodo-1-(5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one
- '[(2R,3S,4S,5R)-5-(4-amino-5-iodo-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 5IC
structure: O[C@H]1[C@@H](O)[C@@H](O[C@H]1n1cc(I)c(nc1=O)N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
5JO:
id: 5JO
name: 2'-o-prop-2-yn-1-yladenosine 5'-(dihydrogen phosphate)
synonyms:
- '[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-prop-2-ynoxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- 2'-O-prop-2-yn-1-yladenosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 5JO
structure: C#CCO[C@@H]1[C@H](O)[C@H](O[C@H]1n1cnc2c1ncnc2N)COP(=O)(O)O
6F7:
id: 6F7
name: 3'-deoxy-5-methyluridine 5'-(dihydrogen phosphate)
synonyms:
- '[(2~{S},4~{R},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- 3'-deoxy-5-methyluridine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 6F7
structure: O[C@@H]1C[C@@H](O[C@@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)(O)O
6FC:
id: 6FC
name: 2'-trifluoromethylthio-2'-deoxycytidine
synonyms:
- 4-azanyl-1-[(2R,3R,4R,5R)-4-oxidanyl-3-(trifluoromethylsulfanyl)-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]pyrimidin-2-one
- 2'-thio-2'-S-(trifluoromethyl)-5'-O-(trihydroxy-lambda~5~-phosphanyl)cytidine
identifiers:
- ns: pdb-ccd
id: 6FC
structure: O[C@@H]1[C@H](COP(O)(O)O)O[C@H]([C@@H]1SC(F)(F)F)n1ccc(nc1=O)N
6FU:
id: 6FU
name: 2'-trifluoromethylthio-2'-deoxyuridine
synonyms:
- 1-[(2R,3R,4R,5R)-4-oxidanyl-3-(trifluoromethylsulfanyl)-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]pyrimidine-2,4-dione
- 2'-thio-2'-S-(trifluoromethyl)-5'-O-(trihydroxy-lambda~5~-phosphanyl)uridine
identifiers:
- ns: pdb-ccd
id: 6FU
structure: O[C@H]1[C@@H](COP(O)(O)O)O[C@H]([C@@H]1SC(F)(F)F)n1ccc(=O)[nH]c1=O
6IA:
id: 6IA
name: n6-isopentenyl-adenosine-5'-monophosphate
synonyms:
- A
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-[6-(3-methylbutylamino)purin-9-yl]oxolan-2-yl]methyl
dihydrogen phosphate'
- N-(3-methylbutyl)adenosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 6IA
structure: CC(CCNc1ncnc2c1ncn2[C@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)([O-])[O-])C
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 25
l_bond_atoms:
- molecule: Monomer
element: P
position: 28
r_displaced_atoms:
- molecule: Monomer
element: H
position: 25
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
6MZ:
id: 6MZ
name: n6-methyladenosine-5'-monophosphate
synonyms:
- A
- '[(2R,3S,4R,5R)-5-[6-(methylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
- N-methyladenosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 6MZ
structure: CNc1ncnc2c1ncn2[C@@H]1O[C@H]([C@H]([C@H]1O)O)COP(=O)(O)O
base_monomers:
- A
6NW:
id: 6NW
name: 2'-o-methyl-5'-o-thiophosphonoadenosine
synonyms:
- 2'-O-methyl-5'-O-thiophosphonoadenosine
- '[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphinic
acid'
identifiers:
- ns: pdb-ccd
id: 6NW
structure: CO[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cnc2c1ncnc2N)CO[P@](=O)(S)[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 7
r_displaced_atoms:
- molecule: Monomer
element: H
position: 7
6OO:
id: 6OO
name: 2'-o-methyl-5'-o-thiophosphonocytidine
synonyms:
- '[(2~{R},3~{R},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphinic
acid'
identifiers:
- ns: pdb-ccd
id: 6OO
structure: CO[C@H]1[C@H](O)[C@H](O[C@H]1n1ccc(nc1=O)N)CO[P@@](=O)(S)O
base_monomers:
- C
6OP:
id: 6OP
name: 1-[(5e)-5,6-dideoxy-2-o-(2-methoxyethyl)-6-phosphono-beta-d-ribo-hex-5-enofuranosyl]-5-methylpyrimidine-2,4(1h,3h)-dione
synonyms:
- '[(~{E})-2-[(2~{R},3~{R},4~{R},5~{R})-4-(2-methoxyethoxy)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]ethenyl]phosphonic
acid'
- 1-[(5E)-5,6-dideoxy-2-O-(2-methoxyethyl)-6-phosphono-beta-D-ribo-hex-5-enofuranosyl]-5-methylpyrimidine-2,4(1H,3H)-dione
identifiers:
- ns: pdb-ccd
id: 6OP
structure: COCCO[C@H]1[C@H](O)[C@H](O[C@@H]1n1cc(C)c(=O)[nH]c1=O)/C=C/[P@@](=O)(O)[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 10
r_displaced_atoms:
- molecule: Monomer
element: H
position: 10
73W:
id: 73W
name: 5'-o-[(dithiophosphono)]cytidine
synonyms:
- 5'-O-[(dithiophosphono)]cytidine
- 4-azanyl-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[[oxidanyl(sulfanyl)phosphinothioyl]oxymethyl]oxolan-2-yl]pyrimidin-2-one
identifiers:
- ns: pdb-ccd
id: 73W
structure: O[C@H]1[C@@H](O)[C@@H](O[C@H]1n1ccc(nc1=O)N)CO[P@@](=S)(S)O
base_monomers:
- C
75B:
id: 75B
name: 5-selenophen-2-yluridine 5'-(dihydrogen phosphate)
synonyms:
- 5-selenophen-2-yluridine 5'-(dihydrogen phosphate)
- '[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)-5-selenophen-2-yl-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 75B
structure: O[C@H]1[C@H](O)[C@H](O[C@H]1n1cc(c2ccc[se]2)c(=O)[nH]c1=O)CO[P@](=O)(O)[O-]
base_monomers:
- U
7AT:
id: 7AT
name: 1-(5-o-phosphono-beta-d-ribofuranosyl)-3-(1h-1,2,3-triazol-5-yl)-1h-pyrazolo[3,4-d]pyrimidin-4-amine
synonyms:
- A
- '[(2R,3S,4R,5R)-5-[4-azanyl-3-(1H-1,2,3-triazol-5-yl)pyrazolo[3,4-d]pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
- 1-(5-O-phosphono-beta-D-ribofuranosyl)-3-(1H-1,2,3-triazol-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
identifiers:
- ns: pdb-ccd
id: 7AT
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1nc(c2c1ncnc2N)c1cnn[nH]1)CO[P@](=O)(O)[O-]
base_monomers:
- A
7MG:
id: 7MG
name: 7n-methyl-8-hydroguanosine-5'-monophosphate
synonyms:
- '[(2R,3S,4R,5R)-5-(2-amino-7-methyl-6-oxo-1,8-dihydropurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- G
- 7-methylguanosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 7MG
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1N1CN(c2c1nc(N)[nH]c2=O)C)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
85Y:
id: 85Y
name: 2'-deoxy-5-{[(naphthalen-2-yl)methyl]carbamoyl}uridine 5'-(dihydrogen phosphate)
synonyms:
- '[(2~{R},3~{S},5~{R})-5-[5-(naphthalen-2-ylmethylcarbamoyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- 2'-deoxy-5-{[(naphthalen-2-yl)methyl]carbamoyl}uridine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: 85Y
structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cc(C(=O)NCc2ccc3c(c2)cccc3)c(=O)[nH]c1=O
base_monomers:
- U
l_bond_atoms:
- molecule: Monomer
element: P
position: 12
l_displaced_atoms:
- molecule: Monomer
element: O
position: 15
charge: -1
8AN:
id: 8AN
name: 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate)
synonyms:
- A
- 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate)
- '[(2S,3S,4R,5R)-3-amino-5-(6-aminopurin-9-yl)-4-hydroxy-oxolan-2-yl]methyl dihydrogen
phosphate'
identifiers:
- ns: pdb-ccd
id: 8AN
structure: N[C@H]1[C@@H](COP(=O)(O)O)O[C@@H]([C@H]1O)n1cnc2c1ncnc2N
base_monomers:
- A
8AZ:
id: 8AZ
name: 8-aza-nebularine-5'-monophosphate
synonyms:
- '[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[(7~{R})-7-oxidanyl-6,7-dihydro-[1,2,3]triazolo[4,5-d]pyrimidin-3-yl]oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 8AZ
structure: O[C@H]1[C@H](O)[C@H](O[C@@H]1n1nnc2c1N=CN[C@H]2O)COP(=O)(O)O
8OS:
id: 8OS
name: 5'-o-[(s)-hydroxy(4-methyl-1h-imidazol-5-yl)phosphoryl]guanosine
synonyms:
- '[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-(4-methyl-1~{H}-imidazol-5-yl)phosphinic
acid'
- 5'-O-[(S)-hydroxy(4-methyl-1H-imidazol-5-yl)phosphoryl]guanosine
identifiers:
- ns: pdb-ccd
id: 8OS
structure: O[C@H]1[C@H](CO[P@@](=O)(c2[nH]cnc2C)O)O[C@@H]([C@@H]1O)n1cnc2c1nc(N)[nH]c2=O
base_monomers:
- G
8RJ:
id: 8RJ
name: (r)-1'-(2',3'-dihydroxypropyl)-thymine
synonyms:
- (2R)-2-hydroxy-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)propyl dihydrogen
phosphate
- '[(2~{R})-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-oxidanyl-propyl]
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 8RJ
structure: O[C@@H](Cn1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
l_bond_atoms:
- molecule: Monomer
element: P
position: 17
l_displaced_atoms:
- molecule: Monomer
element: O
position: 20
charge: -1
9QV:
id: 9QV
name: uridine 2',5'-bis(dihydrogen phosphate)
synonyms:
- uridine 2',5'-bis(dihydrogen phosphate)
- '[(2~{R},3~{R},4~{R},5~{R})-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-5-(phosphonooxymethyl)oxolan-3-yl]
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: 9QV
structure: O[C@@H]1[C@@H](COP(=O)(O)O)O[C@@H]([C@H]1OP(=O)(O)O)n1ccc(=O)[nH]c1=O
base_monomers:
- U
A23:
id: A23
name: adenosine-5'-phosphate-2',3'-cyclic phosphate
synonyms:
- A
- '[(2S,3aR,4R,6R,6aR)-6-(6-amino-9H-purin-9-yl)-2-hydroxy-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]methyl
dihydrogen phosphate'
- '[(1R,3S,5R,6R,8R)-6-(6-aminopurin-9-yl)-3-hydroxy-3-oxo-2,4,7-trioxa-3$l^{5}-phosphabicyclo[3.3.0]octan-8-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: A23
structure: Nc1ncnc2c1ncn2[C@H]1O[C@@H]([C@@H]2[C@H]1O[P@@](=O)(O2)O)COP(=O)([O-])[O-]
base_monomers:
- A
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
A2L:
id: A2L
name: 3'-o-methyoxyethyl-adenosine 5'-monophosphate
synonyms:
- A
- '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-(2-methoxyethoxy)oxolan-2-yl]methyl
dihydrogen phosphate'
- 3'-O-(2-methoxyethyl)adenosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: A2L
structure: COCCO[C@@H]1[C@H](COP(=O)([O-])[O-])O[C@H]([C@@H]1O)n1cnc2c1ncnc2N
base_monomers:
- A
l_bond_atoms:
- molecule: Monomer
element: P
position: 12
l_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
A3P:
id: A3P
name: adenosine-3'-5'-diphosphate
synonyms:
- A
- adenosine 3',5'-bis(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(phosphonooxymethyl)oxolan-3-yl]
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: A3P
structure: O[C@@H]1[C@H](OP(=O)(O)O)[C@H](O[C@@H]1n1cnc2c1ncnc2N)COP(=O)(O)O
base_monomers:
- A
A44:
id: A44
name: 2'-o-methyoxyethyl-adenosine 5'-monophosphate
synonyms:
- A
- 2'-O-(2-methoxyethyl)adenosine 5'-(dihydrogen phosphate)
- '[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-(2-methoxyethoxy)-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: A44
structure: COCCO[C@@H]1[C@@H](O)[C@@H](O[C@@H]1n1cnc2c1ncnc2N)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 10
l_bond_atoms:
- molecule: Monomer
element: P
position: 28
r_displaced_atoms:
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: O
position: 31
charge: -1
A5M:
id: A5M
name: 2'-amine-cytidine-5'-monophosphate
synonyms:
- C
- 2'-amino-2'-deoxycytidine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-4-amino-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: A5M
structure: N[C@H]1[C@@H](O)[C@H](O[C@H]1n1ccc(nc1=O)N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 22
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
A5O:
id: A5O
name: adenine arabinose-5'-phosphate
synonyms:
- A
- 9-(5-O-phosphono-beta-D-arabinofuranosyl)-9H-purin-6-amine
- '[(2R,3S,4S,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen
phosphate'
identifiers:
- ns: pdb-ccd
id: A5O
structure: O[C@@H]1[C@@H](O)[C@H](O[C@@H]1n1cnc2c1ncnc2N)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
A6A:
id: A6A
name: 2-(6-amino-9h-purin-9-yl)-1,5-anhydro-2-deoxy-6-o-phosphono-d-altritol
synonyms:
- 2-(6-amino-9H-purin-9-yl)-1,5-anhydro-2-deoxy-6-O-phosphono-D-altritol
- '[(2R,3S,4S,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxan-2-yl]methyl dihydrogen
phosphate'
identifiers:
- ns: pdb-ccd
id: A6A
structure: O[C@@H]1[C@@H](O)[C@H](OC[C@H]1n1cnc2c1ncnc2N)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
A6C:
id: A6C
name: 2-(4-amino-2-oxopyrimidin-1(2h)-yl)-1,5-anhydro-2-deoxy-6-o-phosphono-d-altritol
synonyms:
- '[(2R,3S,4S,5R)-5-(4-azanyl-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxan-2-yl]methyl
dihydrogen phosphate'
- 2-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,5-anhydro-2-deoxy-6-O-phosphono-D-altritol
identifiers:
- ns: pdb-ccd
id: A6C
structure: O[C@@H]1[C@@H](O)[C@H](OC[C@H]1n1ccc(nc1=O)N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
A6G:
id: A6G
name: 2-(2-amino-6-oxo-1,6-dihydro-9h-purin-9-yl)-1,5-anhydro-2-deoxy-6-o-phosphono-d-altritol
synonyms:
- '[(2R,3S,4S,5R)-5-(2-azanyl-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxan-2-yl]methyl
dihydrogen phosphate'
- 2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-1,5-anhydro-2-deoxy-6-O-phosphono-D-altritol
identifiers:
- ns: pdb-ccd
id: A6G
structure: O[C@@H]1[C@@H](O)[C@H](OC[C@H]1n1cnc2c1nc(N)[nH]c2=O)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
A6U:
id: A6U
name: 1,5-anhydro-2-deoxy-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-6-o-phosphono-d-altritol
synonyms:
- '[(2R,3S,4S,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxan-2-yl]methyl dihydrogen
phosphate'
- 1,5-anhydro-2-deoxy-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-6-O-phosphono-D-altritol
identifiers:
- ns: pdb-ccd
id: A6U
structure: O[C@@H]1[C@@H](O)[C@H](OC[C@H]1n1ccc(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
A7C:
id: A7C
name: 3-[1-(4-bromophenyl)-1h-1,2,3-triazol-4-yl]-1-[5-o-(trihydroxy-lambda~5~-phosphanyl)-beta-d-ribofuranosyl]-1h-pyrazolo[3,4-d]pyrimidin-4-amine
synonyms:
- (2~{R},3~{R},4~{S},5~{R})-2-[4-azanyl-3-[1-(4-bromophenyl)-1,2,3-triazol-4-yl]pyrazolo[3,4-d]pyrimidin-1-yl]-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolane-3,4-diol
- 3-[1-(4-bromophenyl)-1H-1,2,3-triazol-4-yl]-1-[5-O-(trihydroxy-lambda~5~-phosphanyl)-beta-D-ribofuranosyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine
identifiers:
- ns: pdb-ccd
id: A7C
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1nc(c2c1ncnc2N)c1nnn(c1)c1ccc(cc1)Br)COP(O)(O)O
A7E:
id: A7E
name: 3-ethynyl-1-(5-o-phosphono-beta-d-ribofuranosyl)-1h-pyrazolo[3,4-d]pyrimidin-4-amine
synonyms:
- A
- 3-ethynyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
- '[(2R,3S,4R,5R)-5-(4-azanyl-3-ethynyl-pyrazolo[3,4-d]pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: A7E
structure: C#Cc1nn(c2c1c(N)ncn2)[C@H]1O[C@@H]([C@H]([C@H]1O)O)CO[P@](=O)(O)[O-]
base_monomers:
- A
A9Z:
id: A9Z
name: 2'-deoxy-2'-(4-ethyl-1h-1,2,3-triazol-1-yl)adenosine 5'-(dihydrogen phosphate)
synonyms:
- 2'-deoxy-2'-(4-ethyl-1H-1,2,3-triazol-1-yl)adenosine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-(4-ethyl-1,2,3-triazol-1-yl)-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: A9Z
structure: CCc1nnn(c1)[C@@H]1[C@@H](O)[C@H](O[C@H]1n1cnc2c1ncnc2N)COP(=O)(O)O
base_monomers:
- A
ADX:
id: ADX
name: adenosine-5'-phosphosulfate
synonyms:
- '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl sulfo
hydrogen phosphate'
- 5'-O-[(S)-hydroxy(sulfooxy)phosphoryl]adenosine
- N
identifiers:
- ns: pdb-ccd
id: ADX
structure: O[C@@H]1[C@@H](CO[P@@](=O)(OS(=O)(=O)O)O)O[C@@H]([C@@H]1O)n1cnc2c1ncnc2N
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
AP7:
id: AP7
name: n1-protonated adenosine-5'-monophosphate
synonyms:
- A
- '[(2R,3S,4R,5R)-5-(6-azanylpurin-1-ium-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- 5'-adenylic acid
identifiers:
- ns: pdb-ccd
id: AP7
structure: O[C@H]1[C@@H](O)[C@@H](O[C@H]1n1cnc2c1nc[nH+]c2N)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
ATL:
id: ATL
name: '[(1s,3r,4s,7r)-7-hydroxy-3-(thymin-1-yl)-2,5-dioxabicyclo[2.2.1]hept-1-yl]methyl
dihydrogen phosphate'
synonyms:
- '[(1S,4S,5R,7R)-7-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-3,6-dioxabicyclo[2.2.1]heptan-1-yl]methyl
dihydrogen phosphate'
- T
- 1-{2,5-anhydro-4-[(phosphonooxy)methyl]-beta-D-lyxofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione
identifiers:
- ns: pdb-ccd
id: ATL
structure: O[C@H]1[C@H]2OC[C@]1(COP(=O)(O)O)O[C@@H]2n1cc(C)c(=O)[nH]c1=O
B8H:
id: B8H
name: '[(2~{r},3~{s},4~{r},5~{s})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
synonyms:
- '[(2~{R},3~{S},4~{R},5~{S})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
- U
identifiers:
- ns: pdb-ccd
id: B8H
structure: O[C@H]1[C@H](O)[C@H](O[C@@H]1c1cn(C)c(=O)[nH]c1=O)COP(=O)(O)O
base_monomers:
- U
B8K:
id: B8K
name: 7-acetyl, guanosine-5'-monophosphate
synonyms:
- G
- '[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-ethanoyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: B8K
structure: O[C@H]1[C@@H](O)[C@H](O[C@H]1N1CN(c2c1nc(N)[nH]c2=O)C(=O)C)COP(=O)(O)O
base_monomers:
- G
B8N:
id: B8N
name: (2~{r})-2-azanyl-4-[5-[(2~{s},3~{r},4~{s},5~{r})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid
synonyms:
- (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid
identifiers:
- ns: pdb-ccd
id: B8N
structure: OC(=O)[C@H](CCn1c(=O)c(cn(c1=O)C)[C@H]1O[C@@H]([C@H]([C@@H]1O)O)COP(=O)(O)O)N
B8Q:
id: B8Q
name: 3-methyl, cytidine-5'-monophosphate
synonyms:
- C
- '[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-3-methyl-2-oxidanylidene-4~{H}-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: B8Q
structure: O[C@@H]1[C@@H](O)[C@@H](O[C@H]1N1C=C[C@@H](N(C1=O)C)N)COP(=O)(O)O
base_monomers:
- C
B8T:
id: B8T
name: 4-methyl, cytidine-5'-monophosphate
synonyms:
- C
- '[(2~{R},3~{S},4~{R},5~{R})-5-[4-(methylamino)-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: B8T
structure: CNc1ccn(c(=O)n1)[C@H]1O[C@H]([C@@H]([C@H]1O)O)COP(=O)(O)O
base_monomers:
- C
B8W:
id: B8W
name: 6-methyl, guanosine-5'-monophosphate
synonyms:
- G
- '[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-methoxy-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: B8W
structure: COc1nc(N)nc2c1ncn2[C@H]1O[C@H]([C@H]([C@H]1O)O)COP(=O)(O)O
base_monomers:
- G
B9B:
id: B9B
name: 6-propyl, guanosine-5'-monophosphate
synonyms:
- '[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-propoxy-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
- G
identifiers:
- ns: pdb-ccd
id: B9B
structure: CCCOc1nc(N)nc2c1ncn2[C@H]1O[C@H]([C@@H]([C@H]1O)O)COP(=O)(O)O
base_monomers:
- G
B9H:
id: B9H
name: 2'-methyl, 3-propyl, cytidine-5'-monophosphate
synonyms:
- C
- '[(2~{R},3~{R},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-3-propyl-4~{H}-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: B9H
structure: CCCN1[C@@H](N)C=CN(C1=O)[C@H]1O[C@@H]([C@H]([C@H]1OC)O)COP(=O)(O)O
base_monomers:
- C
BGH:
id: BGH
name: '[(2~{r},3~{r},4~{r},5~{r})-5-(2-azanyl-7-ethanoyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
synonyms:
- '[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-ethanoyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- G
identifiers:
- ns: pdb-ccd
id: BGH
structure: CO[C@@H]1[C@@H](O)[C@H](O[C@H]1N1CN(c2c1nc(N)[nH]c2=O)C(=O)C)COP(=O)(O)O
base_monomers:
- G
BMP:
id: BMP
name: 6-hydroxyuridine-5'-phosphate
synonyms:
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-(6-hydroxy-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- 6-hydroxyuridine 5'-(dihydrogen phosphate)
- N
identifiers:
- ns: pdb-ccd
id: BMP
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1c(O)cc(=O)[nH]c1=O)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
BMQ:
id: BMQ
name: 1-(5'-phospho-beta-d-ribofuranosyl)barbituric acid
synonyms:
- 6-oxouridine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-3,4-bis(oxidanyl)-5-[2,4,6-tris(oxidanylidene)-1,3-diazinan-1-yl]oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: BMQ
structure: O=C1CC(=O)N(C(=O)N1)[C@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)(O)O
r_bond_atoms:
- molecule: Monomer
element: O
position: 20
r_displaced_atoms:
- molecule: Monomer
element: H
position: 20
BOE:
id: BOE
name: 2'-o-[2-(benzyloxy)ethyl] thymidine-5'-monophosphate
synonyms:
- 2'-O-[2-(benzyloxy)ethyl]-5-methyluridine 5'-(dihydrogen phosphate)
- '[(2R,3R,4R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-4-(2-phenylmethoxyethoxy)oxolan-2-yl]methyl
dihydrogen phosphate'
- T
identifiers:
- ns: pdb-ccd
id: BOE
structure: O[C@H]1[C@@H](COP(=O)([O-])[O-])O[C@H]([C@H]1OCCOCc1ccccc1)n1cc(C)c(=O)[nH]c1=O
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
l_bond_atoms:
- molecule: Monomer
element: P
position: 8
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
BT5:
id: BT5
name: biotinyl-5-amp
synonyms:
- 5'-O-[(R)-hydroxy({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}oxy)phosphoryl]adenosine
- '[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]
5-[(3aS,4S,6aR)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoate'
- N
identifiers:
- ns: pdb-ccd
id: BT5
structure: O=C1N[C@H]2[C@@H](N1)[C@H](SC2)CCCCC(=O)O[P@](=O)(OC[C@H]1O[C@@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)O
C2L:
id: C2L
name: 5-methyl-3'-o-methoxyethyl cytidine 5'-monophosphate
synonyms:
- C
- '[(2R,3S,4R,5R)-5-(4-amino-5-methyl-2-oxo-pyrimidin-1-yl)-4-hydroxy-3-(2-methoxyethoxy)oxolan-2-yl]methyl
dihydrogen phosphate'
- 3'-O-(2-methoxyethyl)-5-methylcytidine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: C2L
structure: COCCO[C@@H]1[C@@H](COP(=O)([O-])[O-])O[C@@H]([C@@H]1O)n1cc(C)c(nc1=O)N
base_monomers:
- C
l_bond_atoms:
- molecule: Monomer
element: P
position: 12
l_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
C31:
id: C31
name: 2'-o-3-aminopropyl cytidine-5'-monophosphate
synonyms:
- C
- 2'-O-(3-aminopropyl)cytidine 5'-(dihydrogen phosphate)
- '[(2R,3R,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-4-(3-aminopropoxy)-3-hydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: C31
structure: NCCCO[C@@H]1[C@H](O)[C@H](O[C@@H]1n1ccc(nc1=O)N)COP(=O)(O)O
base_monomers:
- C
C43:
id: C43
name: 2'-o-methyoxyethyl-cytidine-5'-monophosphate
synonyms:
- C
- 2'-O-(2-methoxyethyl)cytidine 5'-(dihydrogen phosphate)
- '[(2R,3R,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4-(2-methoxyethoxy)-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: C43
structure: COCCO[C@@H]1[C@H](O)[C@H](O[C@@H]1n1ccc(nc1=O)N)COP(=O)([O-])[O-]
base_monomers:
- C
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
C4J:
id: C4J
name: (5s)-5-{3-[(3s)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-o-phosphono-l-arabinitol
synonyms:
- (5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-L-arabinitol
- (2~{S})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{S})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid
identifiers:
- ns: pdb-ccd
id: C4J
structure: OC(=O)[C@H](CCn1c(=O)c(cn(c1=O)C)[C@H]1O[C@@H]([C@H]([C@@H]1O)O)COP(=O)(O)O)N
C5L:
id: C5L
name: 2'-o-(2-methoxyethyl)-5-methylcytidine 5'-(dihydrogen phosphate)
synonyms:
- '[(2R,3R,4R,5R)-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-4-(2-methoxyethoxy)-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- 2'-O-(2-methoxyethyl)-5-methylcytidine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: C5L
structure: COCCO[C@H]1[C@H](O)[C@@H](O[C@H]1n1cc(C)c(nc1=O)N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 10
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
CAR:
id: CAR
name: cytosine arabinose-5'-phosphate
synonyms:
- C
- 4-amino-1-(5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one
- '[(2R,3S,4S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: CAR
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1ccc(nc1=O)N)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 22
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
CBV:
id: CBV
name: 5-bromocytidine 5'-(dihydrogen phosphate)
synonyms:
- C
- 5-bromocytidine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-5-(4-amino-5-bromo-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: CBV
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cc(Br)c(nc1=O)N)COP(=O)(O)O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
CCC:
id: CCC
name: cytidine-5'-phosphate-2',3'-cyclic phosphate
synonyms:
- C
- '[(1R,3S,5R,6R,8R)-6-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-3-oxo-2,4,7-trioxa-3$l^{5}-phosphabicyclo[3.3.0]octan-8-yl]methyl
dihydrogen phosphate'
- '[(2S,3aR,4R,6R,6aR)-6-(4-amino-2-oxopyrimidin-1(2H)-yl)-2-hydroxy-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: CCC
structure: Nc1ccn(c(=O)n1)[C@H]1O[C@@H]([C@@H]2[C@H]1O[P@@](=O)(O2)O)COP(=O)([O-])[O-]
base_monomers:
- C
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
CG1:
id: CG1
name: 5'-o-[(r)-hydroxy(methoxy)phosphoryl]guanosine
synonyms:
- 5'-O-[(R)-hydroxy(methoxy)phosphoryl]guanosine
- G
- '[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
methyl hydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: CG1
structure: CO[P@](=O)(OC[C@H]1O[C@@H]([C@H]([C@@H]1O)O)n1cnc2c1nc(N)[nH]c2=O)[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 16
r_displaced_atoms:
- molecule: Monomer
element: H
position: 16
CH:
id: CH
name: n3-protonated cytidine-5'-monophosphate
synonyms:
- C
- 5'-cytidylic acid
- '[(2R,3S,4R,5R)-5-(4-amino-2-oxo-3H-pyrimidin-1-ium-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: CH
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1[n+]1ccc([nH]c1=O)N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
CM0:
id: CM0
name: 5-(carboxymethoxy) uridine-5'-monophosphate
synonyms:
- 5-(carboxymethoxy)uridine 5'-(dihydrogen phosphate)
- 2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-2,4-dioxo-pyrimidin-5-yl]oxyethanoic
acid
- N
identifiers:
- ns: pdb-ccd
id: CM0
structure: OC(=O)COc1cn(c(=O)[nH]c1=O)[C@@H]1O[C@@H]([C@@H]([C@@H]1O)O)COP(=O)(O)O
CNU:
id: CNU
name: 5-cyano-uridine-5'-monophosphate
synonyms:
- '[(2R,3S,4R,5R)-5-(5-cyano-2,4-dioxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- 5-cyanouridine 5'-(dihydrogen phosphate)
- U
identifiers:
- ns: pdb-ccd
id: CNU
structure: N#Cc1cn(c(=O)[nH]c1=O)[C@H]1O[C@@H]([C@@H]([C@@H]1O)O)COP(=O)(O)O
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 22
r_displaced_atoms:
- molecule: Monomer
element: H
position: 22
CS8:
id: CS8
name: 3-thiaoctanoyl-coenzyme a
synonyms:
- S-{(9R,13S,15R)-17-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-9,13,15-trihydroxy-10,10-dimethyl-13,15-dioxido-4,8-dioxo-12,14,16-trioxa-3,7-diaza-13,15-diphosphaheptadec-1-yl}
(pentylsulfanyl)ethanethioate (non-preferred name)
- S-[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]ethyl]
2-pentylsulfanylethanethioate
- N
identifiers:
- ns: pdb-ccd
id: CS8
structure: CCCCCSCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(CO[P@](=O)(O[P@](=O)(OC[C@H]1O[C@H]([C@H]([C@H]1OP(=O)(O)O)O)n1cnc2c1ncnc2N)O)O)(C)C)O
CSF:
id: CSF
name: cytidine-5'-monophosphate-3-fluoro-n-acetyl-neuraminic acid
synonyms:
- C
- (3R,4R,5R,6R)-5-acetamido-2-[[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-fluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic
acid
- (2S,3R,4R,5R,6R)-5-(acetylamino)-2-{[(R)-{[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-3-fluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxylic
acid (non-preferred name)
identifiers:
- ns: pdb-ccd
id: CSF
structure: OC[C@H]([C@H]([C@@H]1O[C@](O[P@@](=O)(OC[C@@H]2O[C@H]([C@H]([C@@H]2O)O)n2ccc(nc2=O)N)O)(C(=O)O)[C@H]([C@H]([C@@H]1NC(=O)C)O)F)O)O
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 25
DBM:
id: DBM
name: 9-(6-deoxy-beta-d-allofuranosyl)-6-methylpurine
synonyms:
- 9-(6-deoxy-beta-D-allofuranosyl)-6-methyl-9H-purine
- (2R,3S,4R,5R)-2-(1-hydroxyethyl)-5-(6-methylpurin-9-yl)oxolane-3,4-diol
- N
identifiers:
- ns: pdb-ccd
id: DBM
structure: C[C@@H]([C@H]1O[C@H]([C@H]([C@H]1O)O)n1cnc2c1ncnc2C)O
DJF:
id: DJF
name: "[(1s,5r,6r,8r)-6-(6-aminopurin-9-yl)-2'-(3-oxidanylpropoxy)spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-8-yl]methyl\
\ dihydrogen phosphate"
synonyms:
- "[(1S,5R,6R,8R)-6-(6-aminopurin-9-yl)-2'-(3-oxidanylpropoxy)spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-8-yl]methyl\
\ dihydrogen phosphate"
identifiers:
- ns: pdb-ccd
id: DJF
structure: OCCCOc1cccc2c1[B@-]1(OC2)O[C@H]2[C@@H](O1)[C@@H](O[C@H]2n1cnc2c1ncnc2N)COP(=O)([O-])[O-]
l_bond_atoms:
- molecule: Monomer
element: P
position: 38
l_displaced_atoms:
- molecule: Monomer
element: O
position: 41
charge: -1
E3C:
id: E3C
name: 3-ethyl, cytidine-5'-monophosphate
synonyms:
- C
- '[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-3-ethyl-2-oxidanylidene-4~{H}-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: E3C
structure: CCN1[C@H](N)C=CN(C1=O)[C@H]1O[C@@H]([C@H]([C@@H]1O)O)COP(=O)(O)O
base_monomers:
- C
E6G:
id: E6G
name: 6-ethyl, guanosine-5'-monophosphate
synonyms:
- '[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-ethoxy-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
- G
identifiers:
- ns: pdb-ccd
id: E6G
structure: CCOc1nc(N)nc2c1ncn2[C@@H]1O[C@H]([C@@H]([C@@H]1O)O)COP(=O)(O)O
base_monomers:
- G
E7G:
id: E7G
name: 7-ethyl, guanosine-5'-monophosphate
synonyms:
- G
- '[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-ethyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: E7G
structure: CCN1CN(c2c1c(=O)[nH]c(n2)N)[C@H]1O[C@@H]([C@H]([C@@H]1O)O)COP(=O)(O)O
base_monomers:
- G
EIT:
id: EIT
name: ((3r,4r,5r)-4-(2-(1h-imidazol-1-yl)ethoxy)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-tetrahydrofuran-2-yl)methyl
dihydrogen phosphate
synonyms:
- '[(2R,3R,4R,5R)-3-hydroxy-4-(2-imidazol-1-ylethoxy)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- T
- 2'-O-[2-(1H-imidazol-1-yl)ethyl]-5-methyluridine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: EIT
structure: O[C@H]1[C@@H](COP(=O)([O-])[O-])O[C@H]([C@H]1OCCn1cncc1)n1cc(C)c(=O)[nH]c1=O
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
l_bond_atoms:
- molecule: Monomer
element: P
position: 8
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
ENA:
id: ENA
name: etheno-nad
synonyms:
- '[[(2R,3S,4R,5R)-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-oxidanidyl-phosphoryl]
[(2R,3S,4R,5R)-3,4-dihydroxy-5-(9H-imidazo[2,1-f]purin-6-ium-3-yl)oxolan-2-yl]methyl
phosphate'
identifiers:
- ns: pdb-ccd
id: ENA
structure: O[C@H]1[C@@H](CO[P@](=O)(O[P@@](=O)(OC[C@H]2O[C@@H]([C@@H]([C@@H]2O)O)[n+]2cccc(c2)C(=O)N)[O-])[O-])O[C@H]([C@@H]1O)n1cnc2c1nc[n+]1c2[nH]cc1
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
ENP:
id: ENP
name: etheno-nadp
synonyms:
- '[(2R,3R,4R,5R)-3-hydroxy-5-imidazo[2,1-f]purin-3-yl-4-phosphonooxy-oxolan-2-yl]methyl
[hydroxy-[[(2R,3S,4R,5R)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen
phosphate'
- '[(2R,3R,4R,5R)-3-hydroxy-5-(3H-imidazo[2,1-i]purin-3-yl)-4-(phosphonooxy)tetrahydrofuran-2-yl]methyl
[(2R,3S,4R,5R)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate
(non-preferred name)'
- N
identifiers:
- ns: pdb-ccd
id: ENP
structure: O[C@@H]1[C@@H](CO[P@@](=O)(O[P@@](=O)(OC[C@H]2O[C@@H]([C@@H]([C@@H]2O)O)O)O)O)O[C@@H]([C@@H]1OP(=O)(O)O)n1cnc2c1ncn1c2ncc1
ENQ:
id: ENQ
name: '[[(2r,3s,4r,5r)-3,4-dihydroxy-5-(9h-imidazo[2,1-f]purin-6-ium-3-yl)oxolan-2-yl]methoxy-oxidanidyl-phosphoryl]
[(2r,3s,4r,5r)-3,4-dihydroxy-5-oxidanidyl-oxolan-2-yl]methyl phosphate'
synonyms:
- '[[(2R,3S,4R,5R)-3,4-dihydroxy-5-(9H-imidazo[2,1-f]purin-6-ium-3-yl)oxolan-2-yl]methoxy-oxidanidyl-phosphoryl]
[(2R,3S,4R,5R)-3,4,5-trihydroxyoxolan-2-yl]methyl phosphate'
identifiers:
- ns: pdb-ccd
id: ENQ
structure: O[C@H]1[C@@H](CO[P@@](=O)(O[P@](=O)(OC[C@H]2O[C@H]([C@@H]([C@@H]2O)O)O)[O-])[O-])O[C@H]([C@@H]1O)n1cnc2c1nc[n+]1c2[nH]cc1
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
EQ4:
id: EQ4
name: 5'-o-[(r)-(2-amino-1h-imidazol-1-yl)(hydroxy)phosphoryl]guanosine
synonyms:
- (2-azanylimidazol-1-yl)-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]phosphinic
acid
- 5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]guanosine
identifiers:
- ns: pdb-ccd
id: EQ4
structure: Nc1[nH]c(=O)c2c(n1)n(cn2)[C@@H]1O[C@@H]([C@@H]([C@H]1O)O)CO[P@](=O)(n1ccnc1N)O
base_monomers:
- G
F2T:
id: F2T
name: 2'-deoxy-2'-fluoro-5'-o-thiophosphonouridine
synonyms:
- 2'-deoxy-2'-fluoro-5'-O-thiophosphonouridine
- '[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphinic
acid'
identifiers:
- ns: pdb-ccd
id: F2T
structure: O[C@@H]1[C@@H](CO[P@](=O)(S)[O-])O[C@@H]([C@@H]1F)n1ccc(=O)[nH]c1=O
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
F3N:
id: F3N
name: 3'-deoxy-3'-(l-phenylalanylamino)adenosine 5'-(dihydrogen phosphate)
synonyms:
- '[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3-[[(2S)-2-azanyl-3-phenyl-propanoyl]amino]-4-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- 3'-deoxy-3'-(L-phenylalanylamino)adenosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: F3N
structure: O=C([C@H](Cc1ccccc1)N)N[C@@H]1[C@@H](COP(=O)([O-])[O-])O[C@H]([C@@H]1O)n1cnc2c1ncnc2N
base_monomers:
- A
l_bond_atoms:
- molecule: Monomer
element: P
position: 20
l_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
F3O:
id: F3O
name: 3'-o-l-phenylalanyladenosine 5'-(dihydrogen phosphate)
synonyms:
- '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2S)-2-azanyl-3-phenyl-propanoate'
- 3'-O-L-phenylalanyladenosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: F3O
structure: O=C([C@@H](Cc1ccccc1)N)O[C@@H]1[C@H](COP(=O)(O)O)O[C@H]([C@@H]1O)n1cnc2c1ncnc2N
FA2:
id: FA2
name: 5-(6-amino-9h-purin-9-yl)-4-hydroxytetrahydrofuran-3-yl dihydrogen phosphate
synonyms:
- A
- (3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxytetrahydrofuran-3-yl dihydrogen
phosphate
- '[(3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-oxolan-3-yl] dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: FA2
structure: O[C@@H]1[C@@H](CO[C@H]1n1cnc2c1ncnc2N)OP(=O)([O-])[O-]
l_bond_atoms:
- molecule: Monomer
element: P
position: 21
l_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
FA5:
id: FA5
name: adenosine-5'-[phenylalaninyl-phosphate]
synonyms:
- 5'-O-[(S)-{[(2S)-2-amino-3-phenylpropanoyl]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-3-phenyl-propanoate'
- N
identifiers:
- ns: pdb-ccd
id: FA5
structure: O=C([C@H](Cc1ccccc1)N)O[P@](=O)(OC[C@H]1O[C@@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)[O-]
FAI:
id: FAI
name: 5-(formylamino)-1-(5-o-phosphono-beta-d-ribofuranosyl)-1h-imidazole-4-carboxamide
synonyms:
- 5-(formylamino)-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole-4-carboxamide
- '[(2R,3S,4R,5R)-5-(4-aminocarbonyl-5-formamido-imidazol-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- N
identifiers:
- ns: pdb-ccd
id: FAI
structure: O=CNc1c(ncn1[C@@H]1O[C@H]([C@@H]([C@H]1O)O)COP(=O)([O-])[O-])C(=O)N
r_bond_atoms:
- molecule: Monomer
element: O
position: 19
l_bond_atoms:
- molecule: Monomer
element: P
position: 22
r_displaced_atoms:
- molecule: Monomer
element: H
position: 19
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
FHU:
id: FHU
name: (5s,6r)-5-fluoro-6-hydroxy-pseudouridine-5'-monophosphate
synonyms:
- (1R)-1,4-anhydro-1-[(4R,5S)-5-fluoro-4-hydroxy-2,6-dioxohexahydropyrimidin-5-yl]-5-O-phosphono-D-ribitol
- '[(2R,3S,4R,5R)-5-[(4R,5S)-5-fluoro-4-hydroxy-2,6-dioxo-1,3-diazinan-5-yl]-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- U
identifiers:
- ns: pdb-ccd
id: FHU
structure: O=C1N[C@H](O)[C@@](C(=O)N1)(F)[C@@H]1O[C@H]([C@H]([C@@H]1O)O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 22
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
FMU:
id: FMU
name: 5-fluoro-5-methyluridine-5'-monophosphate
synonyms:
- '[(2R,3S,4R,5R)-5-[(5S)-5-fluoro-5-methyl-2,4-dioxo-1,3-diazinan-1-yl]-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- 5-fluoro-5-methyluridine 5'-(dihydrogen phosphate)
- N
identifiers:
- ns: pdb-ccd
id: FMU
structure: O[C@H]1[C@H](O)[C@@H](O[C@H]1N1C[C@@](C)(F)C(=O)NC1=O)COP(=O)(O)O
G2L:
id: G2L
name: 3'-o-methyoxyethyl-guanosine-5'-monophosphate
synonyms:
- 3'-O-(2-methoxyethyl)guanosine 5'-(dihydrogen phosphate)
- G
- '[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-4-hydroxy-3-(2-methoxyethoxy)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: G2L
structure: COCCO[C@@H]1[C@@H](COP(=O)([O-])[O-])O[C@@H]([C@@H]1O)n1cnc2c1nc(N)[nH]c2=O
base_monomers:
- G
l_bond_atoms:
- molecule: Monomer
element: P
position: 12
l_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
G46:
id: G46
name: guanosine-5'-monothiophosphate
synonyms:
- G
- '[(2R,3S,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphinic
acid'
- 5'-O-thiophosphonoguanosine
identifiers:
- ns: pdb-ccd
id: G46
structure: O[C@H]1[C@H](O)[C@H](O[C@@H]1n1cnc2c1nc(N)[nH]c2=O)CO[P@@](=O)(S)O
base_monomers:
- G
G48:
id: G48
name: 2'-o-methyoxyethyl-guanosine-5'-monophosphate
synonyms:
- 2'-O-(2-methoxyethyl)guanosine 5'-(dihydrogen phosphate)
- G
- '[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-(2-methoxyethoxy)-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: G48
structure: COCCO[C@H]1[C@H](O)[C@H](O[C@@H]1n1cnc2c1nc(N)[nH]c2=O)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 10
l_bond_atoms:
- molecule: Monomer
element: P
position: 30
r_displaced_atoms:
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: O
position: 32
charge: -1
G4P:
id: G4P
name: guanosine-5',3'-tetraphosphate
synonyms:
- guanosine 3',5'-bis(trihydrogen diphosphate)
- '[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-4-hydroxy-3-(hydroxy-phosphonooxy-phosphoryl)oxy-oxolan-2-yl]methyl
phosphono hydrogen phosphate'
- N
identifiers:
- ns: pdb-ccd
id: G4P
structure: O[C@@H]1[C@H](O[P@](=O)(OP(=O)(O)O)O)[C@H](O[C@@H]1n1cnc2c1nc(N)[nH]c2=O)CO[P@@](=O)(OP(=O)(O)O)O
G7M:
id: G7M
name: n7-methyl-guanosine-5'-monophosphate
synonyms:
- G
- '[(2R,3S,4R,5R)-5-(2-amino-7-methyl-6-oxo-1H-purin-7-ium-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- 7-methylguanosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: G7M
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1c[n+](c2c1nc(N)[nH]c2=O)C)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
GAO:
id: GAO
name: guanine arabinose-5'-phosphate
synonyms:
- G
- 2-amino-9-(5-O-phosphono-beta-D-arabinofuranosyl)-1,9-dihydro-6H-purin-6-one
- '[(2R,3S,4S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: GAO
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cnc2c1nc(N)[nH]c2=O)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
GDO:
id: GDO
name: 3'-deoxy-guanosine 5'-monophosphate
synonyms:
- 3'-deoxy-5'-guanylic acid
- '[(2S,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: GDO
structure: O[C@H]1C[C@@H](O[C@H]1n1cnc2c1nc(N)[nH]c2=O)COP(=O)(O)O
base_monomers:
- G
GDP:
id: GDP
name: guanosine-5'-diphosphate
synonyms:
- guanosine 5'-(trihydrogen diphosphate)
- G
- '[(2R,3S,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
phosphono hydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: GDP
structure: O[C@@H]1[C@@H](CO[P@@](=O)(OP(=O)(O)O)O)O[C@@H]([C@@H]1O)n1cnc2c1nc(N)[nH]c2=O
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
GDR:
id: GDR
name: guanosine-5'-diphosphate-rhamnose
synonyms:
- G
- '[[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]
[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyl-oxan-2-yl] hydrogen phosphate'
- '[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl
(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl dihydrogen
diphosphate (non-preferred name)'
identifiers:
- ns: pdb-ccd
id: GDR
structure: O[C@H]1[C@@H](CO[P@@](=O)(O[P@](=O)(O[C@@H]2O[C@@H](C)[C@@H]([C@@H]([C@@H]2O)O)O)O)O)O[C@H]([C@H]1O)n1cnc2c1nc(N)[nH]c2=O
r_bond_atoms:
- molecule: Monomer
element: O
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 27
GH3:
id: GH3
name: 3'-deoxy-guanosine-5'-triphosphate
synonyms:
- G
- '[[(2S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-4-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]
phosphono hydrogen phosphate'
- 3'-deoxyguanosine 5'-(tetrahydrogen triphosphate)
identifiers:
- ns: pdb-ccd
id: GH3
structure: O[C@@H]1C[C@H](O[C@@H]1n1cnc2c1nc(N)[nH]c2=O)CO[P@@](=O)(O[P@@](=O)(OP(=O)(O)O)O)O
base_monomers:
- G
GMU:
id: GMU
name: 2'-o-[(2-guanidinium)ethyl]-5-methyluridine 5'-monophosphate
synonyms:
- 2'-O-{2-[(diaminomethyl)amino]ethyl}-5-methyluridine 5'-(dihydrogen phosphate)
- '[(2R,3R,4R,5R)-4-[2-(diaminomethylamino)ethoxy]-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- U
identifiers:
- ns: pdb-ccd
id: GMU
structure: NC(NCCO[C@H]1[C@H](O)[C@H](O[C@@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)(O)O)N
GOM:
id: GOM
name: glutamol-amp
synonyms:
- (4S)-5-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-oxido-phosphoryl]oxy-4-azaniumyl-pentanoate
- G
- 5'-O-({[(2S)-2-ammonio-4-carboxylatobutyl]oxy}phosphinato)adenosine
identifiers:
- ns: pdb-ccd
id: GOM
structure: '[O-]C(=O)CC[C@H](CO[P@](=O)(OC[C@H]1O[C@H]([C@H]([C@H]1O)O)n1cnc2c1ncnc2N)[O-])[NH3+]'
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 23
GRB:
id: GRB
name: 8-bromoguanosine 5'-(dihydrogen phosphate)
synonyms:
- 8-bromoguanosine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-5-(2-azanyl-8-bromo-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: GRB
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1c(Br)nc2c1nc(N)[nH]c2=O)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
I4U:
id: I4U
name: 4-isopropyl, uridine-5'-monophosphate
synonyms:
- '[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanylidene-4-propan-2-yloxy-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- U
identifiers:
- ns: pdb-ccd
id: I4U
structure: CC(Oc1ccn(c(=O)n1)[C@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)(O)O)C
base_monomers:
- U
IC:
id: IC
name: isocytidine-5'-monophosphate
synonyms:
- C
- '[(2R,3S,4R,5R)-5-(2-amino-4-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- 2-amino-1-(5-O-phosphono-beta-D-ribofuranosyl)pyrimidin-4(1H)-one
identifiers:
- ns: pdb-ccd
id: IC
structure: O[C@@H]1[C@H](O)[C@H](O[C@H]1n1ccc(=O)nc1N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 22
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
IG:
id: IG
name: isoguanosine-5'-monophosphate
synonyms:
- G
- 2-oxoadenosine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-5-(6-amino-2-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: IG
structure: O[C@@H]1[C@H](O)[C@H](O[C@H]1n1cnc2c1nc(=O)[nH]c2N)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
IPN:
id: IPN
name: 2-aminoethylglycine-carbonylmethylene-5-iodouracil
synonyms:
- 2-[carboxymethyl-[2-(5-iodo-2,4-dioxo-pyrimidin-1-yl)ethanoyl]amino]ethylazanium
- 2-{(carboxymethyl)[(5-iodo-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]amino}ethanaminium
- N
identifiers:
- ns: pdb-ccd
id: IPN
structure: '[NH3+]CCN(C(=O)Cn1cc(I)c(=O)[nH]c1=O)CC(=O)O'
IRN:
id: IRN
name: 1-(5-o-phosphono-beta-d-ribofuranosyl)-1h-imidazole
synonyms:
- 1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-imidazol-1-yl-oxolan-2-yl]methyl dihydrogen
phosphate'
- N
identifiers:
- ns: pdb-ccd
id: IRN
structure: O[C@H]1[C@@H](COP(=O)(O)O)O[C@@H]([C@@H]1O)n1cncc1
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
IU:
id: IU
name: 5-iodouridine-5'-monophosphate
synonyms:
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-(5-iodo-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- 5-iodouridine 5'-(dihydrogen phosphate)
- U
identifiers:
- ns: pdb-ccd
id: IU
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cc(I)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
JLN:
id: JLN
name: 5-(formylamino)-1-(5-o-phosphono-beta-d-ribofuranosyl)-1h-imidazole-4-carboxylic
acid
synonyms:
- 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-5-formamido-imidazole-4-carboxylic
acid
identifiers:
- ns: pdb-ccd
id: JLN
structure: O=CNc1c(ncn1[C@@H]1O[C@@H]([C@H]([C@@H]1O)O)COP(=O)(O)O)C(=O)O
JW5:
id: JW5
name: 6-(hydroxymethyl)uridine 5'-(dihydrogen phosphate)
synonyms:
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-[6-(hydroxymethyl)-2,4-dioxo-pyrimidin-1-yl]oxolan-2-yl]methyl
dihydrogen phosphate'
- 6-(hydroxymethyl)uridine 5'-(dihydrogen phosphate)
- N
identifiers:
- ns: pdb-ccd
id: JW5
structure: OCc1cc(=O)[nH]c(=O)n1[C@H]1O[C@@H]([C@@H]([C@@H]1O)O)COP(=O)(O)O
KAG:
id: KAG
name: 2'-deoxy-n-[(1s)-1-methyl-3-oxopropyl]guanosine 5'-phosphate
synonyms:
- 2'-deoxy-N-[(1S)-1-methyl-3-oxopropyl]guanosine 5'-(dihydrogen phosphate)
- '[(2R,3S,5R)-3-hydroxy-5-[6-oxo-2-[[(2S)-4-oxobutan-2-yl]amino]-1H-purin-9-yl]oxolan-2-yl]methyl
dihydrogen phosphate'
- G
identifiers:
- ns: pdb-ccd
id: KAG
structure: O=CC[C@@H](Nc1[nH]c(=O)c2c(n1)n(cn2)[C@@H]1C[C@@H]([C@H](O1)COP(=O)(O)O)O)C
base_monomers:
- G
KGV:
id: KGV
name: 3'-deoxy-3'-(d-phenylalanylamino)adenosine 5'-(dihydrogen phosphate)
synonyms:
- '[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R})-2-azanyl-3-phenyl-propanoyl]amino]-4-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- 3'-deoxy-3'-(D-phenylalanylamino)adenosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: KGV
structure: O=C([C@@H](Cc1ccccc1)N)N[C@H]1[C@@H](COP(=O)([O-])[O-])O[C@H]([C@@H]1O)n1cnc2c1ncnc2N
l_bond_atoms:
- molecule: Monomer
element: P
position: 20
l_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
LCA:
id: LCA
name: '[(1r,3r,4r,7s)-7-hydroxy-3-(adenin-9-yl)-2,5-dioxabicyclo[2.2.1]hept-1-yl]methyl
dihydrogen phosphate'
synonyms:
- A
- 9-{2,5-anhydro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}-9H-purin-6-amine
- '[(1R,4R,6R,7S)-6-(6-aminopurin-9-yl)-7-hydroxy-2,5-dioxabicyclo[2.2.1]heptan-4-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: LCA
structure: O[C@H]1[C@@H]2OC[C@]1(COP(=O)(O)O)O[C@H]2n1cnc2c1ncnc2N
base_monomers:
- A
LCC:
id: LCC
name: '[(1r,3r,4r,7s)-7-hydroxy-3-(5-methylcytosin-1-yl)-2,5-dioxabicyclo[2.2.1]hept-1-yl]methyl
dihydrogen phosphate'
synonyms:
- '[(1R,4R,5R,7S)-5-(4-amino-5-methyl-2-oxo-pyrimidin-1-yl)-7-hydroxy-3,6-dioxabicyclo[2.2.1]heptan-1-yl]methyl
dihydrogen phosphate'
- 4-amino-1-{2,5-anhydro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}-5-methylpyrimidin-2(1H)-one
- N
identifiers:
- ns: pdb-ccd
id: LCC
structure: O[C@@H]1[C@H]2OC[C@]1(COP(=O)(O)O)O[C@H]2n1cc(C)c(nc1=O)N
LCG:
id: LCG
name: '[(1r,3r,4r,7s)-7-hydroxy-3-(guanin-9-yl)-2,5-dioxabicyclo[2.2.1]hept-1-yl]methyl
dihydrogen phosphate'
synonyms:
- G
- 2-amino-9-{2,5-anhydro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}-1,9-dihydro-6H-purin-6-one
- '[(1R,4R,6R,7S)-6-(2-amino-6-oxo-1H-purin-9-yl)-7-hydroxy-2,5-dioxabicyclo[2.2.1]heptan-4-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: LCG
structure: O[C@H]1[C@@H]2OC[C@]1(COP(=O)([O-])[O-])O[C@H]2n1cnc2c1nc(N)[nH]c2=O
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
l_bond_atoms:
- molecule: Monomer
element: P
position: 11
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
LKC:
id: LKC
name: 4-amino-1-[(1s,3r,4r,7s)-7-hydroxy-1-(hydroxymethyl)-2,5-dioxabicyclo[2.2.1]hept-3-yl]-5-methylpyrimidin-2(1h)-one
synonyms:
- 4-amino-1-[2,5-anhydro-4-(hydroxymethyl)-alpha-L-lyxofuranosyl]-5-methylpyrimidin-2(1H)-one
- 4-amino-1-[(1R,4S,6R,7S)-7-hydroxy-4-(hydroxymethyl)-2,5-dioxabicyclo[2.2.1]heptan-6-yl]-5-methyl-pyrimidin-2-one
- N
identifiers:
- ns: pdb-ccd
id: LKC
structure: Cc1cn([C@@H]2O[C@]3([C@H]([C@H]2OC3)O)CO)c(=O)nc1N
LMS:
id: LMS
name: '[(2r,3s,4r,5r)-5-(6-amino-9h-purin-9-yl)-3,4-dihydroxytetrahydro-2-furanyl]methyl
sulfamate'
synonyms:
- '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl sulfamate'
- 5'-O-sulfamoyladenosine
- N
identifiers:
- ns: pdb-ccd
id: LMS
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cnc2c1ncnc2N)COS(=O)(=O)N
M1Y:
id: M1Y
name: (1s)-1,4-anhydro-1-(1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-o-phosphono-d-xylitol
synonyms:
- (1S)-1,4-anhydro-1-(1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-xylitol
- '[(2~{R},3~{R},4~{R},5~{S})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: M1Y
structure: O[C@@H]1[C@H](O)[C@H](O[C@H]1c1cn(C)c(=O)[nH]c1=O)COP(=O)(O)O
M3O:
id: M3O
name: 3'-o-(n-formyl-l-methionyl)adenosine 5'-(dihydrogen phosphate)
synonyms:
- '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
(2S)-2-formamido-4-methylsulfanyl-butanoate'
- 3'-O-(N-formyl-L-methionyl)adenosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: M3O
structure: CSCC[C@H](C(=O)O[C@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@H]1O)n1cnc2c1ncnc2N)NC=O
M5M:
id: M5M
name: 2'-(n-acetamide)-cytidine-5'-monophosphate
synonyms:
- C
- 2'-(acetylamino)-2'-deoxycytidine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-4-acetamido-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: M5M
structure: CC(=O)N[C@@H]1[C@@H](O)[C@H](O[C@H]1n1ccc(nc1=O)N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 9
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
M7A:
id: M7A
name: 7-methyl, adenosine-5'-monophosphate
synonyms:
- A
- '[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-7-methyl-8~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: M7A
structure: O[C@@H]1[C@@H](O)[C@@H](O[C@@H]1N1CN(c2c1ncnc2N)C)COP(=O)(O)O
base_monomers:
- A
MGQ:
id: MGQ
name: 7-benzyl guanine monophosphate
synonyms:
- A
- 7-benzylguanosine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-5-[2-amino-6-oxo-7-(phenylmethyl)-1H-purin-7-ium-9-yl]-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: MGQ
structure: O[C@H]1[C@@H](O)[C@H](O[C@@H]1n1c[n+](c2c1nc(N)[nH]c2=O)Cc1ccccc1)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
MGV:
id: MGV
name: p-fluoro-7-benzyl guanine monophosphate
synonyms:
- '[(2R,3S,4R,5R)-5-[2-amino-7-[(4-fluorophenyl)methyl]-6-oxo-1H-purin-7-ium-9-yl]-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- G
- 7-(4-fluorobenzyl)guanosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: MGV
structure: O[C@H]1[C@@H](O)[C@H](O[C@@H]1n1c[n+](c2c1nc(N)[nH]c2=O)Cc1ccc(cc1)F)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 34
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 36
charge: -1
MHG:
id: MHG
name: 2-methyl, 7-(3-methyl-pentane), guanosine-5'-monophosphate
synonyms:
- '[(2~{R},3~{S},4~{R},5~{R})-5-[2-(methylamino)-7-[(3~{S})-3-methylpentyl]-6-oxidanylidene-1,8-dihydropurin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
- G
identifiers:
- ns: pdb-ccd
id: MHG
structure: CC[C@H](CCN1CN(c2c1c(=O)[nH]c(n2)NC)[C@@H]1O[C@H]([C@@H]([C@H]1O)O)COP(=O)(O)O)C
base_monomers:
- G
MIA:
id: MIA
name: 2-methylthio-n6-isopentenyl-adenosine-5'-monophosphate
synonyms:
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-[6-(3-methylbutylamino)-2-methylsulfanyl-purin-9-yl]oxolan-2-yl]methyl
dihydrogen phosphate'
- A
- N-(3-methylbutyl)-2-(methylsulfanyl)adenosine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: MIA
structure: CSc1nc(NCCC(C)C)c2c(n1)n(cn2)[C@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 28
l_bond_atoms:
- molecule: Monomer
element: P
position: 31
r_displaced_atoms:
- molecule: Monomer
element: H
position: 28
l_displaced_atoms:
- molecule: Monomer
element: O
position: 33
charge: -1
MTU:
id: MTU
name: 9-beta-d-ribofuranosyl-9h-purin-2-amine
synonyms:
- '[(2R,3S,4R,5R)-5-(2-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen
phosphate'
- A
- 9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purin-2-amine
identifiers:
- ns: pdb-ccd
id: MTU
structure: O[C@H]1[C@@H](O)[C@H](O[C@H]1n1cnc2c1nc(N)nc2)COP(=O)(O)O
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
MUM:
id: MUM
name: 5'-o-(dihydroxyphosphanyl)-5-methyl-5,6-dihydrouridine
synonyms:
- '[(2~{R},3~{S},4~{R},5~{R})-5-[(5~{R})-5-methyl-2,4-bis(oxidanylidene)-1,3-diazinan-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphite'
- 5'-O-(dihydroxyphosphanyl)-5-methyl-5,6-dihydrouridine
identifiers:
- ns: pdb-ccd
id: MUM
structure: OP(OC[C@H]1O[C@@H]([C@H]([C@@H]1O)O)N1C[C@@H](C)C(=O)NC1=O)O
N5M:
id: N5M
name: 5-nitrocytidine 5'-(dihydrogen phosphate)
synonyms:
- C
- 5-nitrocytidine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-5-(4-amino-5-nitro-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: N5M
structure: O[C@H]1[C@@H](O)[C@H](O[C@@H]1n1cc([N+](=O)[O-])c(nc1=O)N)COP(=O)([O-])[O-]
base_monomers:
- C
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
N6G:
id: N6G
name: ((2r,3s,4r,5s)-5-(2,6-diamino-9h-purin-9-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl)methyl
dihydrogen phosphate
synonyms:
- G
- 2-aminoadenosine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-5-(2,6-diaminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen
phosphate'
identifiers:
- ns: pdb-ccd
id: N6G
structure: Nc1nc(N)c2c(n1)n(cn2)[C@@H]1O[C@@H]([C@@H]([C@@H]1O)O)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 22
l_bond_atoms:
- molecule: Monomer
element: P
position: 25
r_displaced_atoms:
- molecule: Monomer
element: H
position: 22
l_displaced_atoms:
- molecule: Monomer
element: O
position: 28
charge: -1
NF2:
id: NF2
name: (1s)-1,4-anhydro-1-(2,4-difluoro-5-methylphenyl)-5-o-phosphono-d-ribitol
synonyms:
- (1S)-1,4-anhydro-1-(2,4-difluoro-5-methylphenyl)-5-O-phosphono-D-ribitol
- '[(2R,3S,4R,5S)-5-(2,4-difluoro-5-methyl-phenyl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- N
identifiers:
- ns: pdb-ccd
id: NF2
structure: O[C@H]1[C@@H](O)[C@H](O[C@@H]1c1cc(C)c(cc1F)F)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
O2C:
id: O2C
name: 3'-deoxy-cytidine-5'-monophosphate
synonyms:
- '[(2S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-4-hydroxy-oxolan-2-yl]methyl dihydrogen
phosphate'
- 3'-deoxy-5'-cytidylic acid
- N
identifiers:
- ns: pdb-ccd
id: O2C
structure: O[C@H]1C[C@H](O[C@H]1n1ccc(nc1=O)N)COP(=O)(O)O
O2G:
id: O2G
name: 2'-deoxy-n,n-dimethyl-5'-o-[oxido(oxo)phosphonio]guanosine
synonyms:
- 2'-deoxy-N,N-dimethylguanosine 5'-(dihydrogen phosphate)
- '[(2R,3S,5R)-5-(2-dimethylamino-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- G
identifiers:
- ns: pdb-ccd
id: O2G
structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1cnc2c1nc([nH]c2=O)N(C)C
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
OAD:
id: OAD
name: 2'-o-acetyl adenosine-5-diphosphoribose
synonyms:
- '[(2S,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxymethyl]-2,4-dihydroxy-oxolan-3-yl]
ethanoate'
- (2S,3R,4R,5R)-5-({[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-2,4-dihydroxytetrahydrofuran-3-yl
acetate (non-preferred name)
- N
identifiers:
- ns: pdb-ccd
id: OAD
structure: CC(=O)O[C@@H]1[C@@H](O)O[C@@H]([C@H]1O)CO[P@@](=O)(O[P@@](=O)(OC[C@H]1O[C@@H]([C@@H]([C@@H]1O)O)n1cnc2c1ncnc2N)O)O
ODP:
id: ODP
name: 4-oxo-nicotinamide-adenine dinucleotide phosphate
synonyms:
- '[[(2R,3S,4R,5R)-5-(3-aminocarbonyl-4-oxo-3H-pyridin-1-ium-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]
[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-4-phosphonooxy-oxolan-2-yl]methyl
hydrogen phosphate'
- N
identifiers:
- ns: pdb-ccd
id: ODP
structure: O[C@H]1[C@@H](O)[C@H](O[C@@H]1[N+]1=C[C@H](C(=O)C=C1)C(=O)N)CO[P@@](=O)(O[P@@](=O)(OC[C@@H]1O[C@@H]([C@H]([C@H]1O)OP(=O)(O)O)n1cnc2c1ncnc2N)O)O
ONE:
id: ONE
name: 1-(beta-d-ribofuranosyl)-pyridin-4-one-5'-phosphate
synonyms:
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-oxopyridin-1-yl)oxolan-2-yl]methyl dihydrogen
phosphate'
- 1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-4(1H)-one
- U
identifiers:
- ns: pdb-ccd
id: ONE
structure: O[C@@H]1[C@@H](O)[C@H](O[C@@H]1n1ccc(=O)cc1)COP(=O)([O-])[O-]
base_monomers:
- U
l_bond_atoms:
- molecule: Monomer
element: P
position: 21
l_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
OOB:
id: OOB
name: 5'-o-[(r)-(benzoyloxy)(hydroxy)phosphoryl]adenosine
synonyms:
- 5'-O-[(R)-(benzoyloxy)(hydroxy)phosphoryl]adenosine
- '[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]
benzoate'
identifiers:
- ns: pdb-ccd
id: OOB
structure: O[C@@H]1[C@H](CO[P@@](=O)(OC(=O)c2ccccc2)O)O[C@H]([C@@H]1O)n1cnc2c1ncnc2N
P1P:
id: P1P
name: 3-{[oxido(oxo)phosphino]oxy}propan-1-olate
synonyms:
- 3-(oxido-oxo-phosphaniumyl)oxypropan-1-olate
- (3-oxidopropoxy)(oxo)phosphoniumolate
- N
identifiers:
- ns: pdb-ccd
id: P1P
structure: '[O-]CCCO[P+](=O)[O-]'
P2T:
id: P2T
name: 2'-o-propyl thymidine-5-monophosphate
synonyms:
- '[(2R,3R,4R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-4-propoxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- 5-methyl-2'-O-propyluridine 5'-(dihydrogen phosphate)
- T
identifiers:
- ns: pdb-ccd
id: P2T
structure: CCCO[C@H]1[C@@H](O)[C@H](O[C@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 9
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
r_displaced_atoms:
- molecule: Monomer
element: H
position: 9
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
P4U:
id: P4U
name: 4-propyl, uridine-5'-monophosphate
synonyms:
- '[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanylidene-4-propoxy-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- U
identifiers:
- ns: pdb-ccd
id: P4U
structure: CCCOc1ccn(c(=O)n1)[C@H]1O[C@H]([C@@H]([C@H]1O)O)COP(=O)(O)O
base_monomers:
- U
P5P:
id: P5P
name: purine riboside-5'-monophosphate
synonyms:
- A
- 9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-purin-9-yl-oxolan-2-yl]methyl dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: P5P
structure: O[C@H]1[C@@H](O)[C@@H](O[C@H]1n1cnc2c1ncnc2)COP(=O)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
P7G:
id: P7G
name: 7-propyl, guanosine-5'-monophosphate
synonyms:
- G
- '[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-7-propyl-3,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: P7G
structure: CCCN1CN(c2c1c(=O)nc([nH]2)N)[C@@H]1O[C@H]([C@@H]([C@H]1O)O)COP(=O)(O)O
base_monomers:
- G
PGP:
id: PGP
name: guanosine-3',5'-diphosphate
synonyms:
- '[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-4-hydroxy-2-(phosphonooxymethyl)oxolan-3-yl]
dihydrogen phosphate'
- G
- guanosine 3',5'-bis(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: PGP
structure: O[C@@H]1[C@H](OP(=O)(O)O)[C@H](O[C@@H]1n1cnc2c1nc(N)[nH]c2=O)COP(=O)([O-])[O-]
base_monomers:
- G
l_bond_atoms:
- molecule: Monomer
element: P
position: 30
l_displaced_atoms:
- molecule: Monomer
element: O
position: 33
charge: -1
PMT:
id: PMT
name: phosphoric acid mono-[3-(3-{[5-(4-amino-2-oxo-2h-pyrimidin-1-yl)-3,4- dihydroxy-tetrahydro-furan-2-
ylmethoxy]-hydroxy-phosphoryloxy}-3-oxo-propylcarbamoyl)-3-hydroxy-2,2- dimethyl-propyl]
ester
synonyms:
- C
- 5'-O-{(S)-hydroxy[(3-{[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]amino}propanoyl)oxy]phosphoryl}cytidine
- '[[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]
3-[[(2R)-2-hydroxy-3,3-dimethyl-4-phosphonooxy-butanoyl]amino]propanoate'
identifiers:
- ns: pdb-ccd
id: PMT
structure: O=C(O[P@](=O)(OC[C@H]1O[C@@H]([C@@H]([C@@H]1O)O)n1ccc(nc1=O)N)O)CCNC(=O)[C@@H](C(COP(=O)(O)O)(C)C)O
base_monomers:
- C
PPU:
id: PPU
name: puromycin-5'-monophosphate
synonyms:
- A
- '[(2S,3S,4R,5R)-3-[[(2S)-2-amino-3-(4-methoxyphenyl)propanoyl]amino]-5-(6-dimethylaminopurin-9-yl)-4-hydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- 3'-deoxy-N,N-dimethyl-3'-[(O-methyl-L-tyrosyl)amino]adenosine 5'-(dihydrogen
phosphate)
identifiers:
- ns: pdb-ccd
id: PPU
structure: COc1ccc(cc1)C[C@H](C(=O)N[C@@H]1[C@@H](COP(=O)([O-])[O-])O[C@@H]([C@@H]1O)n1cnc2c1ncnc2N(C)C)N
base_monomers:
- A
l_bond_atoms:
- molecule: Monomer
element: P
position: 21
l_displaced_atoms:
- molecule: Monomer
element: O
position: 24
charge: -1
PQ1:
id: PQ1
name: phosphoric acid mono-[5-(2-amino-5-aminomethyl-4-oxo-3,5-dihydro-4h-pyrido[2,3-d]pyrimidin-8-yl)-3,4-dihydroxy-tetrahydro-furan-2-ylmethyl]
ester
synonyms:
- '[(2R,3S,4R,5R)-5-[2-amino-5-(aminomethyl)-4-oxo-3H-pyrrolo[2,3-d]pyrimidin-7-yl]-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- 2-amino-5-(aminomethyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
- N
identifiers:
- ns: pdb-ccd
id: PQ1
structure: NCc1cn(c2c1c(=O)[nH]c(n2)N)[C@@H]1O[C@@H]([C@@H]([C@@H]1O)O)COP(=O)([O-])[O-]
l_bond_atoms:
- molecule: Monomer
element: P
position: 28
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
PU:
id: PU
name: puromycin-n-aminophosphonic acid
synonyms:
- A
- '[[(2S)-1-[[(2S,3S,4R,5R)-5-(6-dimethylaminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]amino]-3-(4-methoxyphenyl)-1-oxo-propan-2-yl]amino]phosphonic
acid'
- 3'-deoxy-N,N-dimethyl-3'-[(O-methyl-N-phosphono-L-tyrosyl)amino]adenosine
identifiers:
- ns: pdb-ccd
id: PU
structure: OC[C@H]1O[C@@H]([C@@H]([C@@H]1NC(=O)[C@H](NP(=O)([O-])[O-])Cc1ccc(cc1)OC)O)n1cnc2c1ncnc2N(C)C
base_monomers:
- A
l_bond_atoms:
- molecule: Monomer
element: P
position: 18
l_displaced_atoms:
- molecule: Monomer
element: O
position: 21
charge: -1
PUY:
id: PUY
name: puromycin
synonyms:
- (2S)-2-amino-N-[(2S,3S,4R,5R)-5-(6-dimethylaminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]-3-(4-methoxyphenyl)propanamide
- 3'-deoxy-N,N-dimethyl-3'-[(O-methyl-L-tyrosyl)amino]adenosine
- N
identifiers:
- ns: pdb-ccd
id: PUY
structure: OC[C@H]1O[C@H]([C@H]([C@H]1NC(=O)[C@H](Cc1ccc(cc1)OC)N)O)n1cnc2c1ncnc2N(C)C
PYO:
id: PYO
name: 1-(beta-d-ribofuranosyl)-pyrimidin-2-one-5'-phosphate
synonyms:
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-oxopyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen
phosphate'
- 1-(5-O-phosphono-beta-D-ribofuranosyl)pyrimidin-2(1H)-one
- U
identifiers:
- ns: pdb-ccd
id: PYO
structure: O[C@H]1[C@H](O)[C@H](O[C@@H]1n1cccnc1=O)COP(=O)([O-])[O-]
base_monomers:
- U
l_bond_atoms:
- molecule: Monomer
element: P
position: 21
l_displaced_atoms:
- molecule: Monomer
element: O
position: 23
charge: -1
PYY:
id: PYY
name: d-ribofuranosyl-benzene-5'-monophosphate
synonyms:
- '[(2R,3S,4R,5S)-3,4-dihydroxy-5-phenyl-oxolan-2-yl]methyl dihydrogen phosphate'
- (1S)-1,4-anhydro-1-phenyl-5-O-phosphono-D-ribitol
- N
identifiers:
- ns: pdb-ccd
id: PYY
structure: O[C@H]1[C@@H](O)[C@H](O[C@H]1c1ccccc1)COP(=O)(O)O
QUO:
id: QUO
name: 2-amino-7-deaza-(2'',3''-dihydroxy-cyclopentylamino)-guanosine-5'-monophosphate
synonyms:
- G
- 2-amino-5-({[(1R,2S,3R)-2,3-dihydroxycyclopentyl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
- '[(2R,3S,4R,5R)-5-[2-amino-5-[[[(1R,2S,3R)-2,3-dihydroxycyclopentyl]amino]methyl]-4-oxo-3H-pyrrolo[2,3-d]pyrimidin-7-yl]-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: QUO
structure: O[C@H]1[C@@H](O)[C@H](O[C@H]1n1cc(c2c1nc(N)[nH]c2=O)CN[C@@H]1CC[C@@H]([C@@H]1O)O)COP(=O)([O-])[O-]
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 38
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 41
charge: -1
RPC:
id: RPC
name: cytidine 3',5'-bis(dihydrogen phosphate)
synonyms:
- cytidine 3',5'-bis(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl]
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: RPC
structure: O[C@@H]1[C@H](OP(=O)(O)O)[C@@H](O[C@H]1n1ccc(nc1=O)N)COP(=O)(O)O
base_monomers:
- C
RTP:
id: RTP
name: ribavirin triphosphate
synonyms:
- 1-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-1H-1,2,4-triazole-3-carboxamide
- '[[(2R,3S,4R,5R)-5-(3-aminocarbonyl-1,2,4-triazol-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]
phosphono hydrogen phosphate'
- N
identifiers:
- ns: pdb-ccd
id: RTP
structure: O[C@H]1[C@@H](CO[P@@](=O)(O[P@@](=O)(OP(=O)(O)O)O)O)O[C@H]([C@H]1O)n1cnc(n1)C(=O)N
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
RUS:
id: RUS
name: 1-(5-o-phosphono-beta-d-ribofuranosyl)-2-selanylpyrimidin-4(1h)-one
synonyms:
- '[(2R,3S,4R,5R)-3,4-bis(oxidanyl)-5-(4-oxidanylidene-2-selanyl-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- 1-(5-O-phosphono-beta-D-ribofuranosyl)-2-selanylpyrimidin-4(1H)-one
identifiers:
- ns: pdb-ccd
id: RUS
structure: O[C@@H]1[C@@H](O)[C@H](O[C@H]1n1ccc(=O)nc1[SeH])COP(=O)(O)O
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
RY:
id: RY
name: 5'-3,6-dihydrocytidylic acid
synonyms:
- 5'-3,6-dihydrocytidylic acid
- '[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-1,4-dihydropyrimidin-3-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: RY
structure: NC1=CCN(C(=O)N1)[C@@H]1O[C@H]([C@@H]([C@@H]1O)O)COP(=O)(O)O
S2M:
id: S2M
name: 2'-o-[2-(methoxy)ethyl]-2-thiothymidine-5'-monophosphate
synonyms:
- 1-[2-O-(2-methoxyethyl)-5-O-phosphono-beta-D-ribofuranosyl]-5-methyl-2-thioxo-2,3-dihydropyrimidin-4(1H)-one
- T
- '[(2R,3R,4R,5R)-3-hydroxy-4-(2-methoxyethoxy)-5-(5-methyl-4-oxo-2-sulfanylidene-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: S2M
structure: COCCO[C@@H]1[C@@H](O)[C@H](O[C@H]1n1cc(C)c(=O)[nH]c1=S)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 10
l_bond_atoms:
- molecule: Monomer
element: P
position: 28
r_displaced_atoms:
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: O
position: 31
charge: -1
S4C:
id: S4C
name: 4'-thio-4'-deoxy-cytosine-5'-monophosphate
synonyms:
- C
- 4'-thiocytidine 5'-(dihydrogen phosphate)
- '[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-thiolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: S4C
structure: O[C@H]1[C@@H](O)[C@@H](S[C@H]1n1ccc(nc1=O)N)COP(=O)(O)O
base_monomers:
- C
S8M:
id: S8M
name: (2~{r},3~{r},4~{s},5~{s})-2-(6-aminopurin-9-yl)-5-[[(3~{s})-3-azanyl-3-(1~{h}-1,2,3,4-tetrazol-5-yl)propyl]sulfanylmethyl]oxolane-3,4-diol
synonyms:
- (2~{R},3~{R},4~{S},5~{S})-2-(6-aminopurin-9-yl)-5-[[(3~{S})-3-azanyl-3-(1~{H}-1,2,3,4-tetrazol-5-yl)propyl]sulfanylmethyl]oxolane-3,4-diol
identifiers:
- ns: pdb-ccd
id: S8M
structure: O[C@@H]1[C@H](CSCC[C@@H](c2nnn[nH]2)N)O[C@@H]([C@H]1O)n1cnc2c1ncnc2N
SMT:
id: SMT
name: 2'-[(methylthio)ethyloxy]-thymidine-5'-monophosphate
synonyms:
- 5-methyl-2'-O-[2-(methylsulfanyl)ethyl]uridine 5'-(dihydrogen phosphate)
- T
- '[(2R,3R,4R,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-(2-methylsulfanylethoxy)-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: SMT
structure: CSCCO[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)(O)O
SRA:
id: SRA
name: adenosine -5'-thio-monophosphate
synonyms:
- A
- 5'-O-thiophosphonoadenosine
- (2R,3R,4S,5R)-2-(6-aminopurin-9-yl)-5-(dihydroxyphosphinothioyloxymethyl)oxolane-3,4-diol
identifiers:
- ns: pdb-ccd
id: SRA
structure: O[C@H]1[C@H](O)[C@H](O[C@@H]1n1cnc2c1ncnc2N)COP(=S)([O-])[O-]
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 24
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 27
charge: -1
SSU:
id: SSU
name: uridine-5'-phosphorothioate
synonyms:
- 5'-O-thiophosphonouridine
- 1-[(2R,3R,4S,5R)-5-(dihydroxyphosphinothioyloxymethyl)-3,4-dihydroxy-oxolan-2-yl]pyrimidine-2,4-dione
- U
identifiers:
- ns: pdb-ccd
id: SSU
structure: O[C@@H]1[C@H](O)[C@@H](O[C@H]1n1ccc(=O)[nH]c1=O)COP(=S)(O)O
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
SUR:
id: SUR
name: 1-(beta-d-ribofuranosyl)-2-thio-uracil-5'-phosphate
synonyms:
- 1-(5-O-phosphono-beta-D-ribofuranosyl)-2-thioxo-2,3-dihydropyrimidin-4(1H)-one
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-oxo-2-sulfanylidene-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- U
identifiers:
- ns: pdb-ccd
id: SUR
structure: O[C@H]1[C@@H](O)[C@H](O[C@H]1n1ccc(=O)[nH]c1=S)COP(=O)([O-])[O-]
base_monomers:
- U
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
l_displaced_atoms:
- molecule: Monomer
element: O
position: 26
charge: -1
T2T:
id: T2T
name: '[(2s,3s,5r)-3-[(2s)-3-({[(2r,3s,4r,5r)-3-hydroxy-4-methoxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)tetrahydrofuran-2-yl]methyl}amino)-2-methyl-3-oxopropyl]-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)tetrahydrofuran-2-yl]methyl
dihydrogen phosphate'
synonyms:
- '[(2S,3S,5R)-3-[(2S)-3-({[(2R,3R,4R,5R)-3-hydroxy-4-methoxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl}amino)-2-methyl-3-oxopropyl]-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl
dihydrogen phosphate (non-preferred name)'
- '[(2S,3S,5R)-3-[(2S)-3-[[(2R,3R,4R,5R)-3-hydroxy-4-methoxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methylamino]-2-methyl-3-oxo-propyl]-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- N
identifiers:
- ns: pdb-ccd
id: T2T
structure: CO[C@H]1[C@@H](O)[C@H](O[C@@H]1n1cc(C)c(=O)[nH]c1=O)CNC(=O)[C@@H](C[C@@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cc(C)c(=O)[nH]c1=O)C
r_bond_atoms:
- molecule: Monomer
element: O
position: 7
l_bond_atoms:
- molecule: Monomer
element: P
position: 40
r_displaced_atoms:
- molecule: Monomer
element: H
position: 7
l_displaced_atoms:
- molecule: Monomer
element: O
position: 43
charge: -1
T38:
id: T38
name: 2'-o-ethoxymethylene thymidine 5'-monophosphate
synonyms:
- 2'-O-(ethoxymethyl)-5-methyluridine 5'-(dihydrogen phosphate)
- T
- '[(2R,3R,4R,5R)-4-(ethoxymethoxy)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: T38
structure: CCOCO[C@@H]1[C@H](O)[C@H](O[C@@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)(O)O
T39:
id: T39
name: 2'-o-methoxyethylene thymidine 5'-monophosphate
synonyms:
- 2'-O-(2-methoxyethyl)-5-methyluridine 5'-(dihydrogen phosphate)
- '[(2R,3R,4R,5R)-4-(2-methoxyethoxy)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- T
identifiers:
- ns: pdb-ccd
id: T39
structure: COCCO[C@H]1[C@H](O)[C@@H](O[C@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
r_bond_atoms:
- molecule: Monomer
element: O
position: 10
l_bond_atoms:
- molecule: Monomer
element: P
position: 28
r_displaced_atoms:
- molecule: Monomer
element: H
position: 10
l_displaced_atoms:
- molecule: Monomer
element: O
position: 31
charge: -1
T41:
id: T41
name: 1-(2-o-methyl-beta-d-arabinofuranosyl)thymidine 5'-monophosphate
synonyms:
- '[(2R,3R,4S,5R)-4-methoxy-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- T
- 5-methyl-1-(2-O-methyl-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione
identifiers:
- ns: pdb-ccd
id: T41
structure: CO[C@H]1[C@H](O)[C@@H](O[C@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)(O)O
T6A:
id: T6A
name: n-[n-(9-b-d-ribofuranosylpurin-6-yl)carbamoyl]threonine-5'-monophosphate
synonyms:
- A
- (2S,3R)-2-{[(9-{(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-9H-purin-6-yl)carbamoyl]amino}-3-hydroxybutanoic
acid (non-preferred name)
- (2S,3R)-2-[[9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]carbamoylamino]-3-hydroxy-butanoic
acid
identifiers:
- ns: pdb-ccd
id: T6A
structure: O=C(Nc1ncnc2c1ncn2[C@H]1O[C@@H]([C@H]([C@H]1O)O)COP(=O)([O-])[O-])N[C@@H](C(=O)O)[C@@H](O)C
base_monomers:
- A
r_bond_atoms:
- molecule: Monomer
element: O
position: 23
l_bond_atoms:
- molecule: Monomer
element: P
position: 26
r_displaced_atoms:
- molecule: Monomer
element: H
position: 23
l_displaced_atoms:
- molecule: Monomer
element: O
position: 29
charge: -1
TAL:
id: TAL
name: 9-(6-deoxy-alpha-l-talofuranosyl)-6-methylpurine
synonyms:
- 9-(6-deoxy-alpha-L-talofuranosyl)-6-methyl-9H-purine
- (2R,3S,4R,5R)-2-(1-hydroxyethyl)-5-(6-methylpurin-9-yl)oxolane-3,4-diol
- N
identifiers:
- ns: pdb-ccd
id: TAL
structure: C[C@@H]([C@H]1O[C@H]([C@H]([C@H]1O)O)n1cnc2c1ncnc2C)O
TFE:
id: TFE
name: 2'-o-[2-(trifluoro)ethyl] thymidine-5'-monophosphate
synonyms:
- '[(2R,3R,4R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-4-(2,2,2-trifluoroethoxy)oxolan-2-yl]methyl
dihydrogen phosphate'
- 5-methyl-2'-O-(2,2,2-trifluoroethyl)uridine 5'-(dihydrogen phosphate)
- T
identifiers:
- ns: pdb-ccd
id: TFE
structure: O[C@H]1[C@@H](COP(=O)([O-])[O-])O[C@H]([C@H]1OCC(F)(F)F)n1cc(C)c(=O)[nH]c1=O
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
l_bond_atoms:
- molecule: Monomer
element: P
position: 8
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: O
position: 11
charge: -1
TLB:
id: TLB
name: 2'-o,3'-c-methylene-arabinofuranosyl-thymine-5'-monophosphate
synonyms:
- '[(1R,2R,4R,5S)-1-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,6-dioxabicyclo[3.2.0]hept-2-yl]methyl
dihydrogen phosphate'
- '[(1R,2R,4R,5S)-1-hydroxy-4-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-3,6-dioxabicyclo[3.2.0]heptan-2-yl]methyl
dihydrogen phosphate'
- N
identifiers:
- ns: pdb-ccd
id: TLB
structure: O=c1[nH]c(=O)n(cc1C)[C@H]1O[C@@H]([C@]2([C@H]1OC2)O)COP(=O)(O)O
TLN:
id: TLN
name: '[(1r,3r,4r,7s)-7-hydroxy-3-(thymin-1-yl)-2,5-dioxabicyclo[2.2.1]hept-1-yl]methyl
dihydrogen phosphate'
synonyms:
- 1-{2,5-anhydro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione
- '[(1R,4R,5R,7S)-7-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-3,6-dioxabicyclo[2.2.1]heptan-1-yl]methyl
dihydrogen phosphate'
- U
identifiers:
- ns: pdb-ccd
id: TLN
structure: O[C@@H]1[C@H]2OC[C@]1(COP(=O)([O-])[O-])O[C@H]2n1cc(C)c(=O)[nH]c1=O
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
l_bond_atoms:
- molecule: Monomer
element: P
position: 11
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
TPG:
id: TPG
name: 2,2,7-trimethyl-guanosine-5'-triphosphate-5'-guanosine
synonyms:
- '[[[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]
[(2R,3S,4R,5R)-5-(2-dimethylamino-7-methyl-6-oxo-1,8-dihydropurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
hydrogen phosphate'
- G
identifiers:
- ns: pdb-ccd
id: TPG
structure: Nc1[nH]c(=O)c2c(n1)n(cn2)[C@H]1O[C@@H]([C@H]([C@H]1O)O)CO[P@@](=O)(O[P@@](=O)(O[P@@](=O)(OC[C@H]1O[C@@H]([C@H]([C@H]1O)O)N1CN(c2c1nc([nH]c2=O)N(C)C)C)O)O)O
base_monomers:
- G
TYU:
id: TYU
name: tetrahydrouridine
synonyms:
- (4R)-4-hydroxy-1-beta-D-ribofuranosyltetrahydropyrimidin-2(1H)-one
- (4R)-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1,3-diazinan-2-one
- N
identifiers:
- ns: pdb-ccd
id: TYU
structure: OC[C@H]1O[C@H]([C@H]([C@H]1O)O)N1CC[C@@H](NC1=O)O
U2L:
id: U2L
name: 5-methyl-3'-o-methoxyethyl uridine-5'-monophosphate
synonyms:
- '[(2R,3S,4R,5R)-4-hydroxy-3-(2-methoxyethoxy)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- 3'-O-(2-methoxyethyl)-5-methyluridine 5'-(dihydrogen phosphate)
- U
identifiers:
- ns: pdb-ccd
id: U2L
structure: COCCO[C@@H]1[C@@H](COP(=O)([O-])[O-])O[C@@H]([C@@H]1O)n1cc(C)c(=O)[nH]c1=O
base_monomers:
- U
l_bond_atoms:
- molecule: Monomer
element: P
position: 12
l_displaced_atoms:
- molecule: Monomer
element: O
position: 14
charge: -1
U2P:
id: U2P
name: phosphoric acid mono-[2-(2,4-dioxo-3,4-dihydro-2h-pyrimidin-1-yl)-4-hydroxy-5-hydroxymethyl-tetrahydro-furan-3-yl]
ester
synonyms:
- '[(2R,3R,4R,5R)-2-(2,4-dioxopyrimidin-1-yl)-4-hydroxy-5-(hydroxymethyl)oxolan-3-yl]
dihydrogen phosphate'
- 2'-uridylic acid
- U
identifiers:
- ns: pdb-ccd
id: U2P
structure: OC[C@H]1O[C@H]([C@H]([C@H]1O)OP(=O)(O)O)n1ccc(=O)[nH]c1=O
base_monomers:
- U
U31:
id: U31
name: 2'-o-3-aminopropyl 2'-deoxyuridine-5'-monophosphate
synonyms:
- 2'-O-(3-aminopropyl)uridine 5'-(dihydrogen phosphate)
- '[(2R,3R,4R,5R)-4-(3-aminopropoxy)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- U
identifiers:
- ns: pdb-ccd
id: U31
structure: NCCCO[C@@H]1[C@H](O)[C@H](O[C@@H]1n1ccc(=O)[nH]c1=O)COP(=O)(O)O
base_monomers:
- U
U34:
id: U34
name: uridine 5'-monomethylphosphate
synonyms:
- 1-[(6S)-5-deoxy-6-C-phosphono-beta-D-ribo-hexofuranosyl]pyrimidine-2,4(1H,3H)-dione
- '[2-[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]-1-hydroxy-ethyl]phosphonic
acid'
- U
identifiers:
- ns: pdb-ccd
id: U34
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1ccc(=O)[nH]c1=O)C[C@H](P(=O)(O)O)O
base_monomers:
- U
U36:
id: U36
name: 2'-o-methyoxyethyl-uridine-5'-monophosphate
synonyms:
- 2'-O-(2-methoxyethyl)uridine 5'-(dihydrogen phosphate)
- '[(2R,3R,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-(2-methoxyethoxy)-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- U
identifiers:
- ns: pdb-ccd
id: U36
structure: COCCO[C@@H]1[C@H](O)[C@H](O[C@@H]1n1ccc(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
l_bond_atoms:
- molecule: Monomer
element: P
position: 27
l_displaced_atoms:
- molecule: Monomer
element: O
position: 30
charge: -1
U37:
id: U37
name: uridine 5'-monothiophosphate
synonyms:
- 5'-O-thiophosphonouridine
- '[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-sulfanyl-phosphinic
acid'
- U
identifiers:
- ns: pdb-ccd
id: U37
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1ccc(=O)[nH]c1=O)CO[P@](=O)(S)O
base_monomers:
- U
U4M:
id: U4M
name: 1-{2,5-dideoxy-2-fluoro-4-[(phosphonooxy)methyl]-alpha-l-lyxofuranosyl}pyrimidine-2,4(1h,3h)-dione
synonyms:
- 1-{2,5-dideoxy-2-fluoro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}pyrimidine-2,4(1H,3H)-dione
- '[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-2-methyl-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: U4M
structure: F[C@@H]1[C@H](O[C@@]([C@@H]1O)(C)CO[P@@](=O)(O)[O-])n1ccc(=O)[nH]c1=O
U5M:
id: U5M
name: 1-(2,6-dideoxy-2-fluoro-5-o-phosphono-alpha-l-talofuranosyl)pyrimidine-2,4(1h,3h)-dione
synonyms:
- 1-(2,6-dideoxy-2-fluoro-5-O-phosphono-alpha-L-talofuranosyl)pyrimidine-2,4(1H,3H)-dione
- '[(1S)-1-[(2S,3R,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]ethyl]
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: U5M
structure: C[C@H]([C@H]1O[C@@H]([C@H]([C@H]1O)F)n1ccc(=O)[nH]c1=O)OP(=O)(O)O
UAR:
id: UAR
name: uracil arabinose-5'-phosphate
synonyms:
- 1-(5-O-phosphono-beta-D-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione
- '[(2R,3S,4S,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- U
identifiers:
- ns: pdb-ccd
id: UAR
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1n1ccc(=O)[nH]c1=O)COP(=O)([O-])[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
l_bond_atoms:
- molecule: Monomer
element: P
position: 23
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
l_displaced_atoms:
- molecule: Monomer
element: O
position: 25
charge: -1
UBD:
id: UBD
name: uridine 3',5'-bis(dihydrogen phosphate)
synonyms:
- '[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-4-hydroxy-3-phosphonooxy-oxolan-2-yl]methyl
dihydrogen phosphate'
- uridine 3',5'-bis(dihydrogen phosphate)
- U
identifiers:
- ns: pdb-ccd
id: UBD
structure: O[C@H]1[C@H](OP(=O)(O)O)[C@H](O[C@@H]1n1ccc(=O)[nH]c1=O)COP(=O)(O)O
base_monomers:
- U
UD5:
id: UD5
name: 5-fluorouridine
synonyms:
- 5'-O-(dihydroxyphosphanyl)-5-fluorouridine
- '[(2R,3S,4R,5R)-5-(5-fluoro-2,4-dioxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
dihydrogen phosphite'
- U
identifiers:
- ns: pdb-ccd
id: UD5
structure: OP(OC[C@H]1O[C@@H]([C@@H]([C@@H]1O)O)n1cc(F)c(=O)[nH]c1=O)O
base_monomers:
- U
UDP:
id: UDP
name: uridine-5'-diphosphate
synonyms:
- uridine 5'-(trihydrogen diphosphate)
- '[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
phosphono hydrogen phosphate'
- N
identifiers:
- ns: pdb-ccd
id: UDP
structure: O[C@@H]1[C@H](CO[P@](=O)(OP(=O)(O)O)O)O[C@H]([C@H]1O)n1ccc(=O)[nH]c1=O
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
UFB:
id: UFB
name: 2'-f,4'-beta-ome uridine 5'-(dihydrogen phosphate)
synonyms:
- '[(2S,3R,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-fluoro-3-hydroxy-2-methoxytetrahydrofuran-2-yl]methyl
dihydrogen phosphate (non-preferred name)'
- '[(2~{S},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-2-methoxy-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: UFB
structure: CO[C@@]1(CO[P@](=O)(O)[O-])O[C@H]([C@H]([C@@H]1O)F)n1ccc(=O)[nH]c1=O
UOA:
id: UOA
name: '[(2r,3s,4r,5r)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-3-hydroxy-2,4-dimethoxytetrahydrofuran-2-yl]methyl
dihydrogen phosphate (non-preferred name)'
synonyms:
- '[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2,4-dimethoxy-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- '[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3-hydroxy-2,4-dimethoxytetrahydrofuran-2-yl]methyl
dihydrogen phosphate (non-preferred name)'
identifiers:
- ns: pdb-ccd
id: UOA
structure: CO[C@H]1[C@@H](O[C@@]([C@@H]1O)(OC)CO[P@](=O)(O)[O-])n1ccc(=O)[nH]c1=O
UOB:
id: UOB
name: 2'-ome,4'beta-ome uridine 5'-(dihydrogen phosphate)
synonyms:
- '[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2,4-dimethoxy-3-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- '[(2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3-hydroxy-2,4-dimethoxytetrahydrofuran-2-yl]methyl
dihydrogen phosphate (non-preferred name)'
identifiers:
- ns: pdb-ccd
id: UOB
structure: CO[C@@H]1[C@H](O[C@]([C@H]1O)(OC)CO[P@](=O)(O)[O-])n1ccc(=O)[nH]c1=O
UPV:
id: UPV
name: 2'-o-{[(2,2-dimethylpropanoyl)oxy]methyl}uridine 5'-(dihydrogen phosphate)
synonyms:
- '[(2R,3R,4R,5R)-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-5-(phosphonooxymethyl)oxolan-3-yl]oxymethyl
2,2-dimethylpropanoate'
- 2'-O-{[(2,2-dimethylpropanoyl)oxy]methyl}uridine 5'-(dihydrogen phosphate)
identifiers:
- ns: pdb-ccd
id: UPV
structure: O[C@H]1[C@H](COP(=O)([O-])[O-])O[C@@H]([C@H]1OCOC(=O)C(C)(C)C)n1ccc(=O)[nH]c1=O
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 1
l_bond_atoms:
- molecule: Monomer
element: P
position: 8
r_displaced_atoms:
- molecule: Monomer
element: H
position: 1
l_displaced_atoms:
- molecule: Monomer
element: O
position: 10
charge: -1
URD:
id: URD
name: 1-((2r,3r,4s,5r)-tetrahydro-3,4-dihydroxy-5-(hydroxymethyl)furan-2-yl)pyridine-2,4(1h,3h)-dione
synonyms:
- 1-beta-D-ribofuranosylpyridine-2,4(1H,3H)-dione
- 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyridine-2,4-dione
- U
identifiers:
- ns: pdb-ccd
id: URD
structure: OC[C@H]1O[C@H]([C@H]([C@H]1O)O)N1C=CC(=O)CC1=O
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 12
r_displaced_atoms:
- molecule: Monomer
element: H
position: 12
URU:
id: URU
name: ((2s,3s,4r,5r)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-3-(2- ((((2r,5r)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-
3,4-dihydroxytetrahydrofuran-2-yl)methyl)amino)-2-oxoethyl)-4- hydroxytetrahydrofuran-2-yl)methyl
phosphate
synonyms:
- '[(2S,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-[2-[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-2-oxidanylidene-ethyl]-4-oxidanyl-oxolan-2-yl]methyl
dihydrogen phosphate'
- '{(2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3-[2-({[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}amino)-2-oxoethyl]-4-hydroxytetrahydrofuran-2-yl}methyl
dihydrogen phosphate (non-preferred name)'
identifiers:
- ns: pdb-ccd
id: URU
structure: O=C(C[C@@H]1[C@@H](COP(=O)(O)O)O[C@@H]([C@H]1O)n1ccc(=O)[nH]c1=O)NC[C@H]1O[C@@H]([C@@H]([C@@H]1O)O)n1ccc(=O)[nH]c1=O
US5:
id: US5
name: 1-(5-o-phosphono-beta-d-ribofuranosyl)-4-selanylpyrimidin-2(1h)-one
synonyms:
- '[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-oxo-4-selanyl-pyrimidin-1-yl)oxolan-2-yl]methyl
dihydrogen phosphate'
- 1-(5-O-phosphono-beta-D-ribofuranosyl)-4-selanylpyrimidin-2(1H)-one
- U
identifiers:
- ns: pdb-ccd
id: US5
structure: O[C@H]1[C@@H](O)[C@H](O[C@H]1n1ccc(nc1=O)[SeH])CO[P@@](=O)(O)[O-]
base_monomers:
- U
r_bond_atoms:
- molecule: Monomer
element: O
position: 6
r_displaced_atoms:
- molecule: Monomer
element: H
position: 6
XTS:
id: XTS
name: 9-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3h-purine-2,6-dione
synonyms:
- xanthosine
- G
- 9-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H-purine-2,6-dione
identifiers:
- ns: pdb-ccd
id: XTS
structure: OC[C@@H]1O[C@@H]([C@@H]([C@@H]1O)O)n1cnc2c1[nH]c(=O)[nH]c2=O
base_monomers:
- G
r_bond_atoms:
- molecule: Monomer
element: O
position: 12
r_displaced_atoms:
- molecule: Monomer
element: H
position: 12
Y5P:
id: Y5P
name: 1-(5-o-phosphono-beta-d-ribofuranosyl)-1,4-dihydropyrimidine
synonyms:
- 1-(5-O-phosphono-beta-D-ribofuranosyl)-1,4-dihydropyrimidine
- '[(2R,3S,4R,5R)-3,4-bis(oxidanyl)-5-(4H-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen
phosphate'
identifiers:
- ns: pdb-ccd
id: Y5P
structure: O[C@@H]1[C@H](O)[C@H](O[C@@H]1N1C=CCN=C1)COP(=O)(O)O
ZAD:
id: ZAD
name: (s)-1'-(2',3'-dihydroxypropyl)-adenine
synonyms:
- A
- '[(2S)-3-(6-aminopurin-9-yl)-2-hydroxy-propyl] dihydrogen phosphate'
- (2S)-3-(6-amino-9H-purin-9-yl)-2-hydroxypropyl dihydrogen phosphate
identifiers:
- ns: pdb-ccd
id: ZAD
structure: O[C@@H](Cn1cnc2c1ncnc2N)COP(=O)(O)O
base_monomers:
- A
ZBC:
id: ZBC
name: (2s)-3-(4-amino-5-bromo-2-oxopyrimidin-1(2h)-yl)-2-hydroxypropyl dihydrogen
phosphate
synonyms:
- C
- '[(2S)-3-(4-amino-5-bromo-2-oxo-pyrimidin-1-yl)-2-hydroxy-propyl] dihydrogen
phosphate'
- (2S)-3-(4-amino-5-bromo-2-oxopyrimidin-1(2H)-yl)-2-hydroxypropyl dihydrogen
phosphate
identifiers:
- ns: pdb-ccd
id: ZBC
structure: O[C@H](Cn1cc(Br)c(nc1=O)N)COP(=O)(O)O
base_monomers:
- C
ZBU:
id: ZBU
name: (s)-1'-(2',3'-dihydroxypropyl)-5-bromo-uracil
synonyms:
- '[(2S)-3-(5-bromo-2,4-dioxo-pyrimidin-1-yl)-2-hydroxy-propyl] dihydrogen phosphate'
- (2S)-3-(5-bromo-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2-hydroxypropyl dihydrogen
phosphate
- U
identifiers:
- ns: pdb-ccd
id: ZBU
structure: O[C@@H](Cn1cc(Br)c(=O)[nH]c1=O)COP(=O)(O)O
base_monomers:
- U
ZCY:
id: ZCY
name: (s)-1'-(2',3'-dihydroxypropyl)-cytosine
synonyms:
- C
- (2S)-3-(4-amino-2-oxopyrimidin-1(2H)-yl)-2-hydroxypropyl dihydrogen phosphate
- '[(2S)-3-(4-amino-2-oxo-pyrimidin-1-yl)-2-hydroxy-propyl] dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: ZCY
structure: O[C@H](Cn1ccc(nc1=O)N)COP(=O)(O)O
base_monomers:
- C
ZGU:
id: ZGU
name: (s)-1'-(2',3'-dihydroxypropyl)-guanine
synonyms:
- G
- (2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-hydroxypropyl dihydrogen
phosphate
- '[(2S)-3-(2-amino-6-oxo-1H-purin-9-yl)-2-hydroxy-propyl] dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: ZGU
structure: O[C@@H](Cn1cnc2c1nc(N)[nH]c2=O)COP(=O)(O)O
base_monomers:
- G
ZHP:
id: ZHP
name: (s)-1'-(2',3'-dihydroxypropyl)-hydroxypyridone
synonyms:
- '[(2S)-2-hydroxy-3-(3-hydroxy-2-methyl-4-oxo-pyridin-1-yl)propyl] dihydrogen
phosphate'
- (2S)-2-hydroxy-3-(3-hydroxy-2-methyl-4-oxopyridin-1(4H)-yl)propyl dihydrogen
phosphate
- N
identifiers:
- ns: pdb-ccd
id: ZHP
structure: O[C@@H](Cn1ccc(=O)c(c1C)O)COP(=O)(O)O
9V9:
id: 9V9
name: 1-{2,5-anhydro-4-[(phosphonooxy)methyl]-alpha-l-lyxofuranosyl}-5-methyl-2-sulfanylidene-2,3-dihydropyrimidin-4(1h)-one
synonyms:
- '[(1~{R},3~{R},4~{R},7~{S})-3-(5-methyl-4-oxidanylidene-2-sulfanylidene-pyrimidin-1-yl)-7-oxidanyl-2,5-dioxabicyclo[2.2.1]heptan-1-yl]methyl
dihydrogen phosphate'
- 1-{2,5-anhydro-4-[(phosphonooxy)methyl]-alpha-L-lyxofuranosyl}-5-methyl-2-sulfanylidene-2,3-dihydropyrimidin-4(1H)-one
identifiers:
- ns: pdb-ccd
id: 9V9
structure: O[C@@H]1[C@@H]2OC[C@@]1(COP(=O)(O)O)O[C@H]2n1cc(C)c(=O)[nH]c1=S
JMH:
id: JMH
name: 3-methylcytidine- 5'-monophosphate
synonyms:
- C
- '[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylidene-3-methyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate'
identifiers:
- ns: pdb-ccd
id: JMH
structure: O[C@@H]1[C@@H](O)[C@@H](O[C@H]1n1ccc(=N)n(c1=O)C)COP(=O)(O)O
base_monomers:
- C
TC:
id: TC
name: 4-azanyl-1-[(2~{r},3~{r},4~{s})-3-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-oxolan-2-yl]pyrimidin-2-one
synonyms:
- 4-azanyl-1-[(2~{R},3~{R},4~{S})-3-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-oxolan-2-yl]pyrimidin-2-one
identifiers:
- ns: pdb-ccd
id: TC
structure: O[C@@H]1[C@H](CO[C@@H]1n1ccc(nc1=O)N)OP(=O)(=O)O
base_monomers:
- C
TG:
id: TG
name: 2-azanyl-9-[(2~{r},3~{r},4~{s})-3-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-oxolan-2-yl]-1~{h}-purin-6-one
synonyms:
- 2-azanyl-9-[(2~{R},3~{R},4~{S})-3-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-oxolan-2-yl]-1~{H}-purin-6-one
identifiers:
- ns: pdb-ccd
id: TG
structure: O[C@H]1[C@@H](CO[C@@H]1n1cnc2c1nc(N)[nH]c2=O)OP(=O)(=O)O
base_monomers:
- G