Structure of PDB 5ha9 Chain B Binding Site BS01

Receptor Information
>5ha9 Chain B (length=351) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAY
SILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQA
KVEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEE
AEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLL
WHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHT
SQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSA
NISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFK
T
Ligand information
Ligand IDTP0
InChIInChI=1S/C20H23N/c1-21(2)15-7-12-20-18-10-5-3-8-16(18)13-14-17-9-4-6-11-19(17)20/h3-6,8-12H,7,13-15H2,1-2H3
InChIKeyKRMDCWKBEZIMAB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CN(C)CCC=C1c2ccccc2CCc3ccccc13
ACDLabs 12.01c3cc2c(/C(c1c(cccc1)CC2)=C/CCN(C)C)cc3
OpenEye OEToolkits 1.7.0CN(C)CCC=C1c2ccccc2CCc3c1cccc3
FormulaC20 H23 N
NameAmitriptyline;
3-(10,11-dihydro-5H-dibenzo[a,d][7]annulen-5-ylidene)-N,N-dimethylpropan-1-amine
ChEMBLCHEMBL629
DrugBankDB00321
ZINCZINC000000968257
PDB chain5ha9 Chain B Residue 406 [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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PDB5ha9 Crystal structure-based discovery of a novel synthesized PARP1 inhibitor (OL-1) with apoptosis-inducing mechanisms in triple-negative breast cancer.
Resolution4.01 Å
Binding residue
(original residue number in PDB)		E102 D109 H201 Y235 S243 Y246
Binding residue
(residue number reindexed from 1)		E103 D110 H202 Y236 S244 Y247
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.78,IC50=1.65uM
Enzymatic activity
Catalytic site (original residue number in PDB) S243 Y246 E327
Catalytic site (residue number reindexed from 1) S244 Y247 E328
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:5ha9, PDBe:5ha9, PDBj:5ha9
PDBsum5ha9
PubMed28442756
UniProtP09874|PARP1_HUMAN Poly [ADP-ribose] polymerase 1 (Gene Name=PARP1)

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