Structure of PDB 8evf Chain A Binding Site BS03

Receptor Information
>8evf Chain A (length=411) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSY
EARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEI
MSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQ
QKEGMRKQGLFQWLDSLLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAG
ISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGAS
VIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQL
PKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQ
LVVSIRVQSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLT
MLFLCATKFSA
Ligand information
Ligand IDDCP
InChIInChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyRGWHQCVHVJXOKC-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
FormulaC9 H16 N3 O13 P3
Name2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL560403
DrugBankDB03258
ZINCZINC000008215945
PDB chain8evf Chain A Residue 501 [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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PDB8evf The peroxidation-derived DNA adduct, 6-oxo-M 1 dG, is a strong block to replication by human DNA polymerase eta.
Resolution2.87 Å
Binding residue
(original residue number in PDB)		D13 M14 C16 F17 F18 Y52 R55 R61 D115
Binding residue
(residue number reindexed from 1)		D11 M12 C14 F15 F16 Y50 R53 R59 D113
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
View graph for
Biological Process
External links
PDB RCSB:8evf, PDBe:8evf, PDBj:8evf
PDBsum8evf
PubMed37468099
UniProtQ9Y253|POLH_HUMAN DNA polymerase eta (Gene Name=POLH)

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