Structure of PDB 2bvx Chain H Binding Site BS03

Receptor Information
>2bvx 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
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETKGQ
PSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSG
GPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQ
F
Ligand information
Ligand ID5CB
InChIInChI=1S/C22H23Cl2N5O2S/c23-15-4-5-18-17(9-15)14(13-32-18)10-27-20(30)12-29-19(24)11-28-21(22(29)31)26-8-6-16-3-1-2-7-25-16/h1-5,7,9,13,19,22,31H,6,8,10-12H2,(H,26,28)(H,27,30)/t19-,22-/m0/s1
InChIKeySOBGXPPOYFFGTK-UGKGYDQZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04ClC1N(C(O)C(=NC1)NCCc2ncccc2)CC(=O)NCc3c4cc(Cl)ccc4sc3
CACTVS 3.341O[CH]1N(CC(=O)NCc2csc3ccc(Cl)cc23)[CH](Cl)CN=C1NCCc4ccccn4
OpenEye OEToolkits 1.5.0c1ccnc(c1)CCNC2=NCC(N(C2O)CC(=O)NCc3csc4c3cc(cc4)Cl)Cl
CACTVS 3.341O[C@@H]1N(CC(=O)NCc2csc3ccc(Cl)cc23)[C@H](Cl)CN=C1NCCc4ccccn4
FormulaC22 H23 Cl2 N5 O2 S
NameN-(5-CHLORO-BENZO[B]THIOPHEN-3-YLMETHYL)-2-[6-CHLORO-OXO-3-(2-PYRIDIN-2-YL-ETHYLAMINO)-2H-PYRAZIN-1-YL]-ACETAMIDE
ChEMBL
DrugBankDB07165
ZINCZINC000053683847
PDB chain2bvx Chain H Residue 1246 [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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PDB2bvx Design and Discovery of Novel, Potent Pyrazinone-Based Thrombin Inhibitors with a Solubilizing P1-P2-Linker
Resolution3.2 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D N98 L99 I174 A190 C191 E192 V213 S214 W215 G216 F227
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 N95 L96 I173 A194 C195 E196 V219 S220 W221 G222 F233
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.70,Ki=2nM
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:2bvx, PDBe:2bvx, PDBj:2bvx
PDBsum2bvx
PubMed
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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