Structure of PDB 3dux Chain H Binding Site BS03

Receptor Information
>3dux Chain H (length=249) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEQPSV
LQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPF
VMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
Ligand information
Ligand ID64U
InChIInChI=1S/C21H30ClN3O2/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/h4,8-9,12,15,18-19H,1-3,5-7,10-11,13-14,23H2,(H,24,26)/t18-,19+/m1/s1
InChIKeyJGFCNVHEEMBVJG-MOPGFXCFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1cc(cc(c1)Cl)CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](CC3CCCCC3)N
OpenEye OEToolkits 1.7.0c1cc(cc(c1)Cl)CNC(=O)C2CCCN2C(=O)C(CC3CCCCC3)N
CACTVS 3.370N[C@H](CC1CCCCC1)C(=O)N2CCC[C@H]2C(=O)NCc3cccc(Cl)c3
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
FormulaC21 H30 Cl N3 O2
Name3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide;
(2S)-1-((2R)-2-amino-3-cyclohexyl-propanoyl)-N-((3-chlorophenyl)methyl)pyrrolidine-2-carboxamide
ChEMBLCHEMBL1198500
DrugBankDB07190
ZINCZINC000039145543
PDB chain3dux Chain H Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dux Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin
Resolution1.6 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D A190 C191 S195 V213 S214 W215 G216 G226 F227
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 A191 C192 S196 V216 S217 W218 G219 G229 F230
Annotation score1
Binding affinityMOAD: Ki=100nM
PDBbind-CN: -logKd/Ki=7.00,Ki=100nM
BindingDB: Ki=100nM
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:3dux, PDBe:3dux, PDBj:3dux
PDBsum3dux
PubMed19520086
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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