Structure of PDB 1bmn Chain H Binding Site BS03

Receptor Information
>1bmn Chain H (length=257) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTA
NVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDA
CEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWI
QKVIDQF
Ligand information
Ligand IDBM9
InChIInChI=1S/C25H34N6O5S/c26-25(27)30-11-3-7-19(15-30)23(33)28-14-20-8-4-12-31(20)24(34)22(16-32)29-37(35,36)21-10-9-17-5-1-2-6-18(17)13-21/h1-2,5-6,9-10,13,19-20,22,29,32H,3-4,7-8,11-12,14-16H2,(H3,26,27)(H,28,33)/t19-,20-,22-/m0/s1
InChIKeyJWNJPEKBZMEXIU-ONTIZHBOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5c1ccc2cc(ccc2c1)S(=O)(=O)NC(CO)C(=O)N3CCCC3CNC(=O)C4CCCN(C4)C(=N)N
ACDLabs 12.01O=C(N2C(CNC(=O)C1CCCN(C(=[N@H])N)C1)CCC2)C(NS(=O)(=O)c4cc3ccccc3cc4)CO
CACTVS 3.385NC(=N)N1CCC[CH](C1)C(=O)NC[CH]2CCCN2C(=O)[CH](CO)N[S](=O)(=O)c3ccc4ccccc4c3
CACTVS 3.385NC(=N)N1CCC[C@@H](C1)C(=O)NC[C@@H]2CCCN2C(=O)[C@H](CO)N[S](=O)(=O)c3ccc4ccccc4c3
OpenEye OEToolkits 1.7.5[H]/N=C(\N)/N1CCC[C@@H](C1)C(=O)NC[C@@H]2CCCN2C(=O)[C@H](CO)NS(=O)(=O)c3ccc4ccccc4c3
FormulaC25 H34 N6 O5 S
Name[S-(R*,R*)]-1-(AMINOIMINOMETHYL)-N-[[1-[N-[(2-NAPHTHALENYLSULFONYL)-L-SERYL]-3-PYRROLIDINYL]METHYL]-3-PIPERIDENECARBOXA MIDE;
BMS-189090
ChEMBLCHEMBL138877
DrugBank
ZINCZINC000003831647
PDB chain1bmn Chain H Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1bmn Crystallographic determination of the structures of human alpha-thrombin complexed with BMS-186282 and BMS-189090.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D L99 C191 E192 V213 S214 W215 G216 E217 G219 C220
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 L96 C201 E202 V225 S226 W227 G228 E229 G230 C231
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.44,Ki=3.6nM
BindingDB: IC50=16nM,Ki=3.6nM
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:1bmn, PDBe:1bmn, PDBj:1bmn
PDBsum1bmn
PubMed8745399
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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