Structure of PDB 3l3m Chain A Binding Site BS01

Receptor Information
>3l3m Chain A (length=348) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSI
LSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKA
EMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAE
IIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWH
GSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQ
GDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANI
SLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFK
Ligand information
Ligand IDA92
InChIInChI=1S/C19H19FN4O/c20-14-10-11(15-5-1-2-9-22-15)7-8-12(14)19-23-16-6-3-4-13(18(21)25)17(16)24-19/h3-4,6-8,10,15,22H,1-2,5,9H2,(H2,21,25)(H,23,24)/t15-/m0/s1
InChIKeyLGVIXHMVSRYWJL-HNNXBMFYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1cc(c2c(c1)nc([nH]2)c3ccc(cc3F)C4CCCCN4)C(=O)N
CACTVS 3.352NC(=O)c1cccc2nc([nH]c12)c3ccc(cc3F)[CH]4CCCCN4
CACTVS 3.352NC(=O)c1cccc2nc([nH]c12)c3ccc(cc3F)[C@@H]4CCCCN4
OpenEye OEToolkits 1.7.0c1cc(c2c(c1)nc([nH]2)c3ccc(cc3F)[C@@H]4CCCCN4)C(=O)N
FormulaC19 H19 F N4 O
Name2-{2-fluoro-4-[(2S)-piperidin-2-yl]phenyl}-1H-benzimidazole-7-carboxamide
ChEMBLCHEMBL1089125
DrugBank
ZINCZINC000049066661
PDB chain3l3m Chain A Residue 351 [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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PDB3l3m Optimization of phenyl-substituted benzimidazole carboxamide poly(ADP-ribose) polymerase inhibitors: identification of (S)-2-(2-fluoro-4-(pyrrolidin-2-yl)phenyl)-1H-benzimidazole-4-carboxamide (A-966492), a highly potent and efficacious inhibitor.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		E102 D105 H201 G202 Y228 Y235 F236 S243 Y246
Binding residue
(residue number reindexed from 1)		E101 D104 H200 G201 Y227 Y234 F235 S242 Y245
Annotation score1
Binding affinityMOAD: Ki=0.006uM
PDBbind-CN: -logKd/Ki=8.22,Ki=6nM
Enzymatic activity
Catalytic site (original residue number in PDB) S243 Y246 E327
Catalytic site (residue number reindexed from 1) S242 Y245 E326
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:3l3m, PDBe:3l3m, PDBj:3l3m
PDBsum3l3m
PubMed20337371
UniProtP09874|PARP1_HUMAN Poly [ADP-ribose] polymerase 1 (Gene Name=PARP1)

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