Structure of PDB 3dhk Chain H Binding Site BS03

Receptor Information
>3dhk Chain H (length=250) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEGQPS
VLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGP
FVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
Ligand information
Ligand ID23U
InChIInChI=1S/C27H28ClN3O2/c28-22-14-7-9-19(17-22)18-30-26(32)23-15-8-16-31(23)27(33)25(29)24(20-10-3-1-4-11-20)21-12-5-2-6-13-21/h1-7,9-14,17,23-25H,8,15-16,18,29H2,(H,30,32)/t23-,25+/m0/s1
InChIKeyLJTKFVOSAVCILF-UKILVPOCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc(cc1)C(c2ccccc2)C(C(=O)N3CCCC3C(=O)NCc4cccc(c4)Cl)N
CACTVS 3.341N[CH](C(c1ccccc1)c2ccccc2)C(=O)N3CCC[CH]3C(=O)NCc4cccc(Cl)c4
ACDLabs 10.04O=C(NCc1cccc(Cl)c1)C4N(C(=O)C(N)C(c2ccccc2)c3ccccc3)CCC4
CACTVS 3.341N[C@H](C(c1ccccc1)c2ccccc2)C(=O)N3CCC[C@H]3C(=O)NCc4cccc(Cl)c4
OpenEye OEToolkits 1.5.0c1ccc(cc1)C(c2ccccc2)[C@H](C(=O)N3CCC[C@H]3C(=O)NCc4cccc(c4)Cl)N
FormulaC27 H28 Cl N3 O2
Namebeta-phenyl-D-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide
ChEMBL
DrugBank
ZINCZINC000013779051
PDB chain3dhk Chain H Residue 1601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dhk Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin
Resolution1.73 Å
Binding residue
(original residue number in PDB)		Y60A W60D A190 C191 S195 V213 S214 W215 G216 E217 F227
Binding residue
(residue number reindexed from 1)		Y47 W50 A192 C193 S197 V217 S218 W219 G220 E221 F231
Annotation score1
Binding affinityMOAD: Ki=47nM
PDBbind-CN: -logKd/Ki=7.33,Ki=47nM
BindingDB: IC50=12nM
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:3dhk, PDBe:3dhk, PDBj:3dhk
PDBsum3dhk
PubMed19520086
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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