Structure of PDB 5vza Chain A Binding Site BS04

Receptor Information
>5vza Chain A (length=327) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLK
ALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTM
KLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLS
TPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITH
PKEGQEAGLLPRVMCRLQDQGLILYHQHAFERSFCIFRLPQPGSWKAVRV
DLVVAPVSQFPFALLSWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQK
TFFQAASEEDIFRHLGLEYLPPEQRNA
Ligand information
Ligand ID2KH
InChIInChI=1S/C9H16N3O14P3/c13-5-1-2-12(9(16)10-5)8-7(15)6(14)4(25-8)3-24-27(17,18)11-28(19,20)26-29(21,22)23/h1-2,4,6-8,14-15H,3H2,(H,10,13,16)(H2,21,22,23)(H3,11,17,18,19,20)/t4-,6-,7-,8-/m1/s1
InChIKeyOZIBFYOFLVBDIY-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
CACTVS 3.385O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.385O[C@H]1[C@@H](O)[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 1.7.6C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O
FormulaC9 H16 N3 O14 P3
Name5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
ChEMBL
DrugBank
ZINCZINC000098208190
PDB chain5vza 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5vza Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu.
Resolution1.501 Å
Binding residue
(original residue number in PDB)		G319 G320 R323 G328 H329 D330 D332 S433 W434 G436 K438
Binding residue
(residue number reindexed from 1)		G182 G183 R186 G191 H192 D193 D195 S266 W267 G269 K271
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D330 D332 D418
Catalytic site (residue number reindexed from 1) D193 D195 D251
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5vza, PDBe:5vza, PDBj:5vza
PDBsum5vza
PubMed28911097
UniProtQ9NP87|DPOLM_HUMAN DNA-directed DNA/RNA polymerase mu (Gene Name=POLM)

[Back to BioLiP]