KarrLab/bpforms

Id,Name,Nucleotide monophosphate,Nucleotide monophosphate (2-) (cleaned),Left bond atom (P),Left displaced atom (O-),Right bond atom (O),Nucleobase,Nucleobase (cleaned),Backbone bond atom,Comments
"1,N2-ethenoG","1,N2-etheno-2'-deoxyguanosine-5'-monophosphate",[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c([H])nc2c1nc1n([H])c([H])c([H])n1c2=O,O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc1[nH]ccn1c2=O,12,15,1,[H]c1nc2c(nc3n([H])c([H])c([H])n3c2=O)[nH]1,O=c1n2cc[nH]c2nc2c1nc[nH]2,14,"Arise as side products of lipid peroxidation under oxidative stress. exocyclic adducts are repaired with an epoxide intermediate, that is hydrolyzed to the repaired base + CHO-CHO."
"1,N6-ethenoA","1,N6-etheno-2'-deoxyadenosine-5'-monophosphate",[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c([H])nc2c1N=C([H])[N]1=C2N([H])C([H])=C1[H],O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc[n+]1c2[nH]cc1,12,15,1,[H]N1C([H])=C([H])N2C([H])=NC3=NC([H])=NC3=C12,c1[nH]c2=NCn3c(=c2n1)[nH]cc3,2,
1eA,1-ethyl-2'-deoxyadenosine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c([H])nc2c1N=C([H])[N](=C2N([H])[H])C([H])([H])C([H])([H])[H],CC[n+]1cnc2c(c1N)ncn2[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O,23,26,27,[H]N([H])C1=C2N=C([H])N=C2N=C([H])N1C([H])([H])C([H])([H])[H],CCN1CN=c2c(=C1N)nc[nH]2,12,
1heA,1-hydroxyethyl-2'-deoxyadenosine-5'-monophosphate,[H]OC([H])([H])C([H])([H])[N]1=C(N([H])[H])c2nc([H])n(c2N=C1[H])[C@]1([H])O[C@]([H])(C([H])([H])OP(O)(O)=O)[C@@]([H])(O[H])C1([H])[H],OCC[n+]1cnc2c(c1N)ncn2[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O,24,27,28,[H]OC([H])([H])C([H])([H])N1C([H])=NC2=NC([H])=NC2=C1N([H])[H],NC1=c2nc[nH]c2=NCN1CCO,6,
1hpA,1-hydroxypropyl-2'-deoxyadenosine-5'-monophosphate,[H]OC([H])([H])C([H])([H])C([H])([H])[N]1=C(N([H])[H])c2nc([H])n(c2N=C1[H])[C@]1([H])O[C@]([H])(C([H])([H])OP(O)(O)=O)[C@@]([H])(O[H])C1([H])[H],OCCC[n+]1cnc2c(c1N)ncn2[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O,25,28,29,[H]OC([H])([H])C([H])([H])C([H])([H])N1C([H])=NC2=NC([H])=NC2=C1N([H])[H],NC1=c2nc[nH]c2=NCN1CCCO,6,
1mA,1-methyl-2'-deoxyadenosine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c([H])nc2c1N=C([H])[N](=C2N([H])[H])C([H])([H])[H],O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc[n+](c2N)C,12,15,1,[H]N([H])C1=C2N=C([H])N=C2N=C([H])N1C([H])([H])[H],Cn1cnc2c(c1N)ncn2,11,Occurs sparsely. Repaired by a direct repair (DR) mechanism. Also repaired in RNA.
1mG,1-methyl-2'-deoxyguanosine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c([H])nc2c1nc(N([H])[H])n(c2=O)C([H])([H])[H],O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc(N)n(c2=O)C,12,15,1,[H]N([H])c1nc2[nH]c([H])nc2c(=O)n1C([H])([H])[H],Cn1c(N)nc2c(c1=O)nc[nH]2,12,Repaired by a direct repair (DR) mechanism.
1pA,1-propyl-2'-deoxyadenosine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c([H])nc2c1N=C([H])[N](=C2N([H])[H])C([H])([H])C([H])([H])C([H])([H])[H],CCC[n+]1cnc2c(c1N)ncn2[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O,24,27,28,[H]N([H])C1=C2N=C([H])N=C2N=C([H])N1C([H])([H])C([H])([H])C([H])([H])[H],CCCN1CN=c2c(=C1N)nc[nH]2,13,
dU,2'-deoxyuridine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c([H])c([H])c(=O)n([H])c1=O,O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1ccc(=O)[nH]c1=O,12,15,1,[H]c1[nH]c(=O)n([H])c(=O)c1[H],O=c1cc[nH]c(=O)[nH]1,5,"Cysteine spontaneously loses an amine group, which is replaced by a keto group at the C4-atom. This reaction occurs spontaneously and all the time, and is the reason why T is used in DNA. This way, dU and T can be distinguished from each other."
2mG,2-methyl-2'-deoxyguanosine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c([H])nc2c1nc(N([H])C([H])([H])[H])n([H])c2=O,CNc1[nH]c(=O)c2c(n1)n(cn2)[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O,24,27,28,[H]N(c1nc2[nH]c([H])nc2c(=O)n1[H])C([H])([H])[H],CNc1[nH]c(=O)c2c(n1)[nH]cn2,11,
"3,N4-ethenoC","3,N4-etheno-2'-deoxycytidine-5'-monophosphate",[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c([H])c([H])c2nc([H])c([H])n2c1=O,O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1ccc2n(c1=O)ccn2,12,15,1,[H]c1nc2c([H])c([H])[nH]c(=O)n2c1[H],O=c1[nH]ccc2n1ccn2,3,
3eC,3-ethyl-2'-deoxycytidine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)N1C([H])=C([H])C(N([H])[H])=[N](C1=O)C([H])([H])C([H])([H])[H],CC[n+]1c(N)ccn(c1=O)[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O,21,24,25,[H]N([H])C1=C([H])C([H])=NC(=O)N1C([H])([H])C([H])([H])[H],CCn1c(N)ccnc1=O,8,
3heC,3-hydroxyethyl-2'-deoxycytidine-5'-monophosphate,[H]OC([H])([H])C([H])([H])[N]1=C(N([H])[H])C([H])=C([H])N(C1=O)[C@]1([H])O[C@]([H])(C([H])([H])OP(O)(O)=O)[C@@]([H])(O[H])C1([H])[H],OCC[n+]1c(N)ccn(c1=O)[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O,22,25,26,[H]OC([H])([H])C([H])([H])N1C(=O)N=C([H])C([H])=C1N([H])[H],NC1C=CNC(=O)N1CCO,5,
3hpC,3-hydroxypropyl-2'-deoxycytidine-5'-monophosphate,[H]OC([H])([H])C([H])([H])C([H])([H])[N]1=C(N([H])[H])C([H])=C([H])N(C1=O)[C@]1([H])O[C@]([H])(C([H])([H])OP(O)(O)=O)[C@@]([H])(O[H])C1([H])[H],OCCC[n+]1c(N)ccn(c1=O)[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O,23,26,27,[H]OC([H])([H])C([H])([H])C([H])([H])N1C(=O)N=C([H])C([H])=C1N([H])[H],NC1C=CNC(=O)N1CCCO,5,
3mA,3-methyl-2'-deoxyadenosine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c([H])nc2c1[N](=C([H])N=C2N([H])[H])C([H])([H])[H],O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1[n+](C)cnc2N,12,15,1,[H]N([H])C1=C2N=C([H])N=C2N(C([H])=N1)C([H])([H])[H],Nc1ncn(c2c1ncn2)C,10,Occurs frequently. Repaired by direct repair (DR) mechanisms. AlkB activity not confirmed. Also repaired by the BER pathway.
3mC,3-methyl-2'-deoxycytidine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)N1C([H])=C([H])C(N([H])[H])=[N](C1=O)C([H])([H])[H],O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1ccc([n+](c1=O)C)N,12,15,1,[H]N([H])C1=C([H])C([H])=NC(=O)N1C([H])([H])[H],Cn1c(N)ccnc1=O,7,Occurs sparsely. Repaired by a direct repair (DR) mechanism. Also repaired in RNA.
3mG,3-methyl-2'-deoxyguanosine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c([H])nc2c1[N](=C(N([H])[H])N([H])C2=O)C([H])([H])[H],O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1[n+](C)c([nH]c2=O)N,12,15,1,[H]N([H])C1=NC(=O)C2N=C([H])N=C2N1C([H])([H])[H],Cn1c(N)nc(=O)c2c1[nH]cn2,10,Occurs sparsely.
3mT,3-methyl-2'-deoxythymidine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c([H])c(c(=O)n(c1=O)C([H])([H])[H])C([H])([H])[H],O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cc(C)c(=O)n(c1=O)C,12,15,1,[H]c1[nH]c(=O)n(c(=O)c1C([H])([H])[H])C([H])([H])[H],Cn1c(=O)c(C)c[nH]c1=O,8,Repaired by a direct repair (DR) mechanism.
3pC,3-propyl-2'-deoxycytidine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)N1C([H])=C([H])C(N([H])[H])=[N](C1=O)C([H])([H])C([H])([H])C([H])([H])[H],CCC[n+]1c(N)ccn(c1=O)[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O,22,25,26,[H]N([H])C1=C([H])C([H])=NC(=O)N1C([H])([H])C([H])([H])C([H])([H])[H],CCCN1C(N)C=CNC1=O,9,
4mC,4-methyl-2'-deoxycytidine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c([H])c([H])c(nc1=O)N([H])C([H])([H])[H],CNc1ccn(c(=O)n1)[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O,20,23,24,[H]N(c1nc(=O)[nH]c([H])c1[H])C([H])([H])[H],CNc1cc[nH]c(=O)n1,6,Repaired by a direct repair (DR) mechanism.
thymidine glycol,"5,6-dihydroxy-5,6-dihydrothymidine-5'-monophosphate",[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)N1C(=O)N([H])C(=O)[C@@](O[H])(C([H])([H])[H])[C@@]1([H])O[H],O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])N1C(=O)NC(=O)[C@]([C@H]1O)(C)O,12,15,1,[H]O[C@@]1([H])NC(=O)N([H])C(=O)[C@@]1(O[H])C([H])([H])[H],O=C1N[C@H](O)[C@@](C(=O)N1)(C)O,3,"One of the principal DNA lesions induced by oxidation and ionizing radiation, has been investigated in Escherichia coli. Thymine glycol was positioned at a unique site in the single-stranded genome of a bacteriophage M13mp19 derivative. Replication of the genome in E. coli yielded targeted mutations at a frequency of 0.3%; the mutations were exclusively T to C transitions."
6mA,6-methyl-2'-deoxyadenosine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c([H])nc2c(nc([H])nc12)N([H])C([H])([H])[H],CNc1ncnc2c1ncn2[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O,22,25,26,[H]N(c1nc([H])nc2[nH]c([H])nc12)C([H])([H])[H],CNc1ncnc2c1nc[nH]2,11,AlkB activity not confirmed
7mA,7-methyl-2'-deoxyadenosine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)N1C([H])=[N](c2c1nc([H])nc2N([H])[H])C([H])([H])[H],O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1c[n+](c2c1ncnc2N)C,12,15,1,[H]N([H])C1=NC([H])=NC2=C1N(C([H])=N2)C([H])([H])[H],Cn1cnc2c1c(N)ncn2,4,Occurs sparsely. AlkB activity not confirmed.
7mG,7-methyl-2'-deoxyguanosine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)N1C([H])=[N](c2c1nc(N([H])[H])n([H])c2=O)C([H])([H])[H],O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1c[n+](c2c1nc(N)[nH]c2=O)C,12,15,1,[H]N([H])C1=NC2=C(N(C([H])=N2)C([H])([H])[H])C(=O)N1[H],CN1CNc2c1c(=O)[nH]c(n2)N,4,Occurs frequently.
8mG,8-methyl-2'-deoxyguanosine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c(nc2c1nc(N([H])[H])n([H])c2=O)C([H])([H])[H],O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1c(C)nc2c1nc(N)[nH]c2=O,12,15,1,[H]N([H])c1nc2[nH]c(nc2c(=O)n1[H])C([H])([H])[H],Cc1[nH]c2c(n1)c(=O)[nH]c(n2)N,3,Repaired by a direct repair (DR) mechanism.
O2mT,O2-methyl-2'-deoxythymidine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)N1C([H])=C(C(=O)N([H])[C@@]1([H])OC([H])([H])[H])C([H])([H])[H],CO[C@@H]1NC(=O)C(=CN1[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O)C,21,24,25,[H]N1C(=O)C(=C([H])N[C@]1([H])OC([H])([H])[H])C([H])([H])[H],CO[C@H]1NC=C(C(=O)N1)C,5,AlkB activity not confirmed.
O4mT,O4-methyl-2'-deoxythymidine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)N1C([H])=C(C([H])([H])[H])[C@]([H])(OC([H])([H])[H])N([H])C1=O,CO[C@@H]1NC(=O)N(C=C1C)[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O,22,25,26,[H]N1C(=O)NC([H])=C(C([H])([H])[H])[C@]1([H])OC([H])([H])[H],CO[C@@H]1NC(=O)NC=C1C,8,Occurs sparsely. Repaired by the NER pathway.
O6mG,O6-methyl-2'-deoxyguanosine-5'-monophosphate,[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(O)(O)=O)n1c([H])nc2c1N=C(N([H])[H])N([H])[C@@]2([H])OC([H])([H])[H],CO[C@@H]1NC(=[NH+]c2c1ncn2[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O)N,24,27,28,[H]N([H])C1=Nc2[nH]c([H])nc2[C@]([H])(OC([H])([H])[H])N1[H],CO[C@@H]1NC(=Nc2c1nc[nH]2)N,12,Occurs frequently. Repaired by a direct repair (DR) mechanism.