Structure of PDB 3rml Chain H Binding Site BS03

Receptor Information
>3rml 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 IDM31
InChIInChI=1S/C22H27ClN4O4S/c23-19-9-8-17(12-24)18(11-19)13-25-22(29)20-7-4-10-27(20)21(28)14-26-32(30,31)15-16-5-2-1-3-6-16/h1-3,5-6,8-9,11,20,26H,4,7,10,12-15,24H2,(H,25,29)/t20-/m0/s1
InChIKeyLCIBXVIGRUMDEF-FQEVSTJZSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NCc1ccc(Cl)cc1CNC(=O)[C@@H]2CCCN2C(=O)CN[S](=O)(=O)Cc3ccccc3
OpenEye OEToolkits 1.7.2c1ccc(cc1)CS(=O)(=O)NCC(=O)N2CCC[C@H]2C(=O)NCc3cc(ccc3CN)Cl
OpenEye OEToolkits 1.7.2c1ccc(cc1)CS(=O)(=O)NCC(=O)N2CCCC2C(=O)NCc3cc(ccc3CN)Cl
CACTVS 3.370NCc1ccc(Cl)cc1CNC(=O)[CH]2CCCN2C(=O)CN[S](=O)(=O)Cc3ccccc3
ACDLabs 12.01O=C(NCc1cc(Cl)ccc1CN)C3N(C(=O)CNS(=O)(=O)Cc2ccccc2)CCC3
FormulaC22 H27 Cl N4 O4 S
NameN-(benzylsulfonyl)glycyl-N-[2-(aminomethyl)-5-chlorobenzyl]-L-prolinamide
ChEMBLCHEMBL2152426
DrugBank
ZINCZINC000095573097
PDB chain3rml 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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PDB3rml Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect
Resolution1.53 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D E97A A190 S195 V213 S214 W215 G216 E217 G219 F227
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 E94 A193 S198 V218 S219 W220 G221 E222 G223 F232
Annotation score1
Binding affinityBindingDB: Ki=1.5nM
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:3rml, PDBe:3rml, PDBj:3rml
PDBsum3rml
PubMed22612268
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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