Structure of PDB 3vyd Chain A Binding Site BS01

Receptor Information
>3vyd Chain A (length=337) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LTLGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSK
CSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVG
GITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQ
GVLKEDVFSFYYNRDSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQI
QMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLF
DYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAM
DIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR
Ligand information
Ligand IDVYD
InChIInChI=1S/C24H37ClN4O2/c1-17(2)9-10-27-23(31)19-11-18(12-26-13-19)14-28-15-22(30)29(16-24(28,3)4)21-8-6-5-7-20(21)25/h5-8,17-19,26H,9-16H2,1-4H3,(H,27,31)/t18-,19+/m1/s1
InChIKeyXGYKQWJDBJCEAW-MOPGFXCFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)CCNC(=O)[C@H]1C[C@H](CNC1)CN2CC(=O)N(CC2(C)C)c3ccccc3Cl
OpenEye OEToolkits 1.7.6CC(C)CCNC(=O)C1CC(CNC1)CN2CC(=O)N(CC2(C)C)c3ccccc3Cl
ACDLabs 12.01Clc3ccccc3N2C(=O)CN(CC1CNCC(C(=O)NCCC(C)C)C1)C(C2)(C)C
CACTVS 3.370CC(C)CCNC(=O)[CH]1CNC[CH](C1)CN2CC(=O)N(CC2(C)C)c3ccccc3Cl
CACTVS 3.370CC(C)CCNC(=O)[C@@H]1CNC[C@@H](C1)CN2CC(=O)N(CC2(C)C)c3ccccc3Cl
FormulaC24 H37 Cl N4 O2
Name(3S,5R)-5-{[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]methyl}-N-(3-methylbutyl)piperidine-3-carboxamide
ChEMBLCHEMBL2204736
DrugBank
ZINCZINC000095563276
PDB chain3vyd Chain A Residue 402 [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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PDB3vyd Design and discovery of new (3S,5R)-5-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]piperidine-3-carboxamides as potent renin inhibitors
Resolution2.81 Å
Binding residue
(original residue number in PDB)		Q19 D38 G40 S41 Y83 T85 F119 F124 D226 G228
Binding residue
(residue number reindexed from 1)		Q19 D38 G40 S41 Y83 T85 F119 F124 D223 G225
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.39,IC50=406nM
BindingDB: IC50=406nM
Enzymatic activity
Catalytic site (original residue number in PDB) D38 S41 N43 W45 Y83 D226 A229
Catalytic site (residue number reindexed from 1) D38 S41 N43 W45 Y83 D223 A226
Enzyme Commision number 3.4.23.15: renin.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function
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Biological Process
External links
PDB RCSB:3vyd, PDBe:3vyd, PDBj:3vyd
PDBsum3vyd
PubMed23122821
UniProtP00797|RENI_HUMAN Renin (Gene Name=REN)

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