Structure of PDB 6nrf Chain A Binding Site BS01

Receptor Information
>6nrf Chain A (length=240) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KSKLPKPVQDLIKMIFGDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKN
THATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFA
GILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLIL
LGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVP
LGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFK
Ligand information
Ligand IDKYV
InChIInChI=1S/C28H25N5O4/c29-26(35)20-5-3-4-19-24(34)23(37-25(19)20)16-17-8-10-18(11-9-17)27(36)32-12-14-33(15-13-32)28-30-21-6-1-2-7-22(21)31-28/h1-11,34H,12-16H2,(H2,29,35)(H,30,31)
InChIKeyFHGOQDSWXMEGJF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC(=O)c1cccc2c(O)c(Cc3ccc(cc3)C(=O)N4CCN(CC4)c5[nH]c6ccccc6n5)oc12
OpenEye OEToolkits 2.0.7c1ccc2c(c1)[nH]c(n2)N3CCN(CC3)C(=O)c4ccc(cc4)Cc5c(c6cccc(c6o5)C(=O)N)O
ACDLabs 12.01N3(CCN(c1nc2c(n1)cccc2)CC3)C(c6ccc(Cc5c(O)c4cccc(C(=O)N)c4o5)cc6)=O
FormulaC28 H25 N5 O4
Name2-({4-[4-(1H-benzimidazol-2-yl)piperazine-1-carbonyl]phenyl}methyl)-3-hydroxy-1-benzofuran-7-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6nrf Chain A Residue 1103 [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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PDB6nrf Design and Synthesis of Poly(ADP-ribose) Polymerase Inhibitors: Impact of Adenosine Pocket-Binding Motif Appendage to the 3-Oxo-2,3-dihydrobenzofuran-7-carboxamide on Potency and Selectivity.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		H862 G863 N868 G888 Y889 Y896 F897 S904 Y907
Binding residue
(residue number reindexed from 1)		H92 G93 N98 G118 Y119 Y126 F127 S134 Y137
Annotation score1
Binding affinityMOAD: ic50=18nM
PDBbind-CN: -logKd/Ki=7.74,IC50=18nM
Enzymatic activity
Catalytic site (original residue number in PDB) S904 Y907 E988
Catalytic site (residue number reindexed from 1) S134 Y137 E218
Enzyme Commision number 2.4.2.-
2.4.2.30: NAD(+) ADP-ribosyltransferase.
Gene Ontology
Molecular Function
GO:0003950 NAD+-protein poly-ADP-ribosyltransferase activity

View graph for
Molecular Function
External links
PDB RCSB:6nrf, PDBe:6nrf, PDBj:6nrf
PDBsum6nrf
PubMed31042381
UniProtP09874|PARP1_HUMAN Poly [ADP-ribose] polymerase 1 (Gene Name=PARP1)

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