Structure of PDB 3f68 Chain H Binding Site BS03

Receptor Information
>3f68 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 ID91U
InChIInChI=1S/C23H32ClN3O3/c1-16(28)26-20(14-17-7-3-2-4-8-17)23(30)27-12-6-11-21(27)22(29)25-15-18-9-5-10-19(24)13-18/h5,9-10,13,17,20-21H,2-4,6-8,11-12,14-15H2,1H3,(H,25,29)(H,26,28)/t20-,21+/m1/s1
InChIKeyNEBILTDHZWSWJN-RTWAWAEBSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(=O)N[CH](CC1CCCCC1)C(=O)N2CCC[CH]2C(=O)NCc3cccc(Cl)c3
CACTVS 3.370CC(=O)N[C@H](CC1CCCCC1)C(=O)N2CCC[C@H]2C(=O)NCc3cccc(Cl)c3
OpenEye OEToolkits 1.7.0CC(=O)NC(CC1CCCCC1)C(=O)N2CCCC2C(=O)NCc3cccc(c3)Cl
OpenEye OEToolkits 1.7.0CC(=O)N[C@H](CC1CCCCC1)C(=O)N2CCC[C@H]2C(=O)NCc3cccc(c3)Cl
ACDLabs 12.01O=C(NCc1cccc(Cl)c1)C3N(C(=O)C(NC(=O)C)CC2CCCCC2)CCC3
FormulaC23 H32 Cl N3 O3
NameN-acetyl-3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide
ChEMBL
DrugBank
ZINCZINC000055398740
PDB chain3f68 Chain H Residue 901 [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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PDB3f68 Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		H57 N98 A190 S195 V213 S214 W215 G216 E217 F227
Binding residue
(residue number reindexed from 1)		H43 N95 A191 S196 V216 S217 W218 G219 E220 F230
Annotation score1
Binding affinityMOAD: Ki=8.7uM
PDBbind-CN: -logKd/Ki=5.06,Ki=8.7uM
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:3f68, PDBe:3f68, PDBj:3f68
PDBsum3f68
PubMed19520086
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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