Structure of PDB 3kjd Chain A Binding Site BS01

Receptor Information
>3kjd Chain A (length=350) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TENLYFQSMDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQI
KAGYQSLKKIEDCIRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQK
ELSEKIQLLEALGDIEIAIKLVKSPEHPLDQHYRNLHCALRPLDHESYEF
KVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHG
SRMSNWVGILSHGLRIAHPEAPITGYMFGKGIYFADMSSKSANYCFASRL
KNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFV
TLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNF
Ligand information
Ligand ID78P
InChIInChI=1S/C13H16N4O/c1-13(6-3-7-15-13)12-16-9-5-2-4-8(11(14)18)10(9)17-12/h2,4-5,15H,3,6-7H2,1H3,(H2,14,18)(H,16,17)/t13-/m1/s1
InChIKeyJNAHVYVRKWKWKQ-CYBMUJFWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1(CCCN1)c2[nH]c3c(cccc3n2)C(=O)N
ACDLabs 10.04O=C(N)c3c1c(nc(n1)C2(NCCC2)C)ccc3
CACTVS 3.341C[C]1(CCCN1)c2[nH]c3c(cccc3C(N)=O)n2
CACTVS 3.341C[C@@]1(CCCN1)c2[nH]c3c(cccc3C(N)=O)n2
OpenEye OEToolkits 1.5.0C[C@@]1(CCCN1)c2[nH]c3c(cccc3n2)C(=O)N
FormulaC13 H16 N4 O
Name(2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium;
Veliparib
ChEMBLCHEMBL506871
DrugBankDB07232
ZINCZINC000084610155
PDB chain3kjd Chain A Residue 1 [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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PDB3kjd Crystal structure of the catalytic domain of human PARP2 in complex with PARP inhibitor ABT-888.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		H428 G429 Y462 S470 Y473
Binding residue
(residue number reindexed from 1)		H199 G200 Y233 S241 Y244
Annotation score1
Binding affinityMOAD: Kd=2.9nM
PDBbind-CN: -logKd/Ki=8.54,Kd=2.9nM
BindingDB: IC50=1.3nM,Kd=5.8nM
Enzymatic activity
Catalytic site (original residue number in PDB) K264 A265 I289 F305 T307 S470 Y473 E558
Catalytic site (residue number reindexed from 1) K39 A40 I64 F80 T82 S241 Y244 E329
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:3kjd, PDBe:3kjd, PDBj:3kjd
PDBsum3kjd
PubMed20092359
UniProtQ9UGN5|PARP2_HUMAN Poly [ADP-ribose] polymerase 2 (Gene Name=PARP2)

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