Structure of PDB 6wid Chain A Binding Site BS05

Receptor Information
>6wid Chain A (length=330) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAAS
VLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERY
QTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQ
DLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFL
ITHPKEGQEAGLLPRVMCRLQDQGLILYHQHAFERSFCIFRLPQPGSWKA
VRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDP
EQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Ligand information
Ligand IDDUP
InChIInChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1
InChIKeyXZLLMTSKYYYJLH-SHYZEUOFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1C[C@@H](O[C@@H]1CO[P@](O)(=O)N[P@](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[CH]1C[CH](O[CH]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
FormulaC9 H16 N3 O13 P3
Name2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
ChEMBLCHEMBL1232397
DrugBankDB01965
ZINC
PDB chain6wid Chain A Residue 701 [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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PDB6wid Structural snapshots of human DNA polymerase mu engaged on a DNA double-strand break.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		G320 R323 G328 H329 D330 D332 G433 W434 G436
Binding residue
(residue number reindexed from 1)		G186 R189 G194 H195 D196 D198 G269 W270 G272
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D330 D332 D418
Catalytic site (residue number reindexed from 1) D196 D198 D254
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0016779 nucleotidyltransferase activity
GO:0034061 DNA polymerase activity
Biological Process
GO:0006281 DNA repair
Cellular Component
GO:0005634 nucleus

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6wid, PDBe:6wid, PDBj:6wid
PDBsum6wid
PubMed32963245
UniProtQ9NP87|DPOLM_HUMAN DNA-directed DNA/RNA polymerase mu (Gene Name=POLM)

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