Structure of PDB 3rm2 Chain H Binding Site BS03

Receptor Information
>3rm2 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 IDS00
InChIInChI=1S/C29H39N5O4S/c30-27(31)24-15-13-22(14-16-24)19-32-28(35)26-12-7-17-34(26)29(36)25(18-21-8-3-1-4-9-21)33-39(37,38)20-23-10-5-2-6-11-23/h2,5-6,10-11,13-16,21,25-26,33H,1,3-4,7-9,12,17-20H2,(H3,30,31)(H,32,35)/t25-,26+/m1/s1
InChIKeyDJNNZKJZFCRFRX-FTJBHMTQSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NC(=N)c1ccc(CNC(=O)[CH]2CCCN2C(=O)[CH](CC3CCCCC3)N[S](=O)(=O)Cc4ccccc4)cc1
OpenEye OEToolkits 1.7.2c1ccc(cc1)CS(=O)(=O)NC(CC2CCCCC2)C(=O)N3CCCC3C(=O)NCc4ccc(cc4)C(=N)N
CACTVS 3.370NC(=N)c1ccc(CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](CC3CCCCC3)N[S](=O)(=O)Cc4ccccc4)cc1
ACDLabs 12.01O=C(NCc1ccc(C(=[N@H])N)cc1)C4N(C(=O)C(NS(=O)(=O)Cc2ccccc2)CC3CCCCC3)CCC4
OpenEye OEToolkits 1.7.2[H]/N=C(/c1ccc(cc1)CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](CC3CCCCC3)NS(=O)(=O)Cc4ccccc4)\\N
FormulaC29 H39 N5 O4 S
NameN-(benzylsulfonyl)-3-cyclohexyl-D-alanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide
ChEMBLCHEMBL1229261
DrugBank
ZINCZINC000058581013
PDB chain3rm2 Chain H Residue 1 [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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PDB3rm2 Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect
Resolution1.23 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D N98 D189 A190 C191 E192 V213 S214 W215 G216 G219 C220
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 N95 D192 A193 C194 E195 V218 S219 W220 G221 G223 C224
Annotation score1
Binding affinityBindingDB: Ki=0.119nM
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:3rm2, PDBe:3rm2, PDBj:3rm2
PDBsum3rm2
PubMed22612268
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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