Structure of PDB 6m7o Chain A Binding Site BS05

Receptor Information
>6m7o Chain A (length=423) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSY
EARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEI
MSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQ
GTVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERET
GFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSL
GGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHD
PVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRND
NDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNT
SGIQTEWSPPLTMLFLCATKFSA
Ligand information
Ligand ID1FZ
InChIInChI=1S/C10H18N3O13P3/c1-5-3-13(10(16)11-9(5)15)8-2-6(14)7(25-8)4-24-27(17,18)12-28(19,20)26-29(21,22)23/h3,6-8,14H,2,4H2,1H3,(H,11,15,16)(H2,21,22,23)(H3,12,17,18,19,20)/t6-,7+,8+/m0/s1
InChIKeyYRKUYVYMPXAOAT-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
CACTVS 3.370CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H18 N3 O13 P3
Name5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine
ChEMBL
DrugBank
ZINCZINC000013455017
PDB chain6m7o Chain A Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6m7o Bypassing a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase eta at atomic resolution.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		D13 M14 C16 F18 Y52 R55 R61 D115 K231
Binding residue
(residue number reindexed from 1)		D11 M12 C14 F16 Y50 R53 R59 D113 K223
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0003684 damaged DNA binding
Biological Process
GO:0006281 DNA repair

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:6m7o, PDBe:6m7o, PDBj:6m7o
PDBsum6m7o
PubMed30275308
UniProtQ9Y253|POLH_HUMAN DNA polymerase eta (Gene Name=POLH)

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