Structure of PDB 2zc9 Chain H Binding Site BS03

Receptor Information
>2zc9 Chain H (length=251) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
G
Ligand information
Ligand ID22U
InChIInChI=1S/C21H24ClN3O2/c22-17-9-4-8-16(12-17)14-24-20(26)19-10-5-11-25(19)21(27)18(23)13-15-6-2-1-3-7-15/h1-4,6-9,12,18-19H,5,10-11,13-14,23H2,(H,24,26)/t18-,19+/m1/s1
InChIKeyCJHLRGCXPGIPCB-MOPGFXCFSA-N
SMILES
SoftwareSMILES
CACTVS 3.370N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCc3cccc(Cl)c3
ACDLabs 12.01O=C(NCc1cccc(Cl)c1)C3N(C(=O)C(N)Cc2ccccc2)CCC3
OpenEye OEToolkits 1.7.0c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3cccc(c3)Cl)N
OpenEye OEToolkits 1.7.0c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NCc3cccc(c3)Cl)N
CACTVS 3.370N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3cccc(Cl)c3
FormulaC21 H24 Cl N3 O2
NameD-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide;
(2S)-1-[(2R)-2-amino-3-phenyl-propanoyl]-N-[(3-chlorophenyl)methyl]pyrrolidine-2-carboxamide
ChEMBLCHEMBL321130
DrugBankDB06919
ZINC
PDB chain2zc9 Chain H Residue 1501 [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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PDB2zc9 Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin
Resolution1.58 Å
Binding residue
(original residue number in PDB)		Y60A W60D N98 A190 C191 V213 S214 W215 G216 F227
Binding residue
(residue number reindexed from 1)		Y47 W50 N95 A193 C194 V218 S219 W220 G221 F232
Annotation score1
Binding affinityMOAD: Ki=180nM
PDBbind-CN: -logKd/Ki=6.74,Ki=180nM
BindingDB: Ki=250nM
Enzymatic activity
Enzyme Commision number 3.4.21.5: thrombin.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0005509 calcium ion binding
Biological Process
GO:0006508 proteolysis
GO:0007596 blood coagulation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2zc9, PDBe:2zc9, PDBj:2zc9
PDBsum2zc9
PubMed19520086
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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