Structure of PDB 7m7l Chain A Binding Site BS06

Receptor Information
>7m7l Chain A (length=427) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGI
IAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASV
EVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYI
EGLPQGTVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAA
IERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIR
KIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCR
GIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLT
KDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVI
KNCNTSGTEWSPPLTMLFLCATKFSAS
Ligand information
Ligand IDDZ4
InChIInChI=1S/C10H17N6O11P3/c11-9-8-10(13-3-12-9)16(4-14-8)7-1-5(17)6(26-7)2-25-28(18,19)15-29(20,21)27-30(22,23)24/h3-7,17H,1-2H2,(H2,11,12,13)(H2,22,23,24)(H3,15,18,19,20,21)/t5-,6+,7+/m0/s1
InChIKeyWKIPJDSLGCBQCU-RRKCRQDMSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H17 N6 O11 P3
Name2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
ChEMBL
DrugBank
ZINCZINC000032016786
PDB chain7m7l Chain A Residue 505 [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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PDB7m7l Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction.
Resolution1.58 Å
Binding residue
(original residue number in PDB)		S257 K293 W297
Binding residue
(residue number reindexed from 1)		S254 K290 W294
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

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Molecular Function
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Biological Process
External links
PDB RCSB:7m7l, PDBe:7m7l, PDBj:7m7l
PDBsum7m7l
PubMed34088846
UniProtQ9Y253|POLH_HUMAN DNA polymerase eta (Gene Name=POLH)

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