Structure of PDB 1mu6 Chain B Binding Site BS03

Receptor Information
>1mu6 Chain B (length=250) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEGQPS
VLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGP
FVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
Ligand information
Ligand IDCDA
InChIInChI=1S/C20H19F3N6O2/c1-13-9-27-18(28-12-20(22,23)16-6-2-3-7-25-16)19(31)29(13)11-17(30)26-10-15-14(21)5-4-8-24-15/h2-9H,10-12H2,1H3,(H,26,30)(H,27,28)
InChIKeyJXHWVKOKYDAROD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN=C(C(=O)N1CC(=O)NCc2c(cccn2)F)NCC(c3ccccn3)(F)F
CACTVS 3.341CC1=CN=C(NCC(F)(F)c2ccccn2)C(=O)N1CC(=O)NCc3ncccc3F
ACDLabs 10.04Fc1cccnc1CNC(=O)CN3C(=CN=C(NCC(F)(F)c2ncccc2)C3=O)C
FormulaC20 H19 F3 N6 O2
Name2-(6-CHLORO-3-{[2,2-DIFLUORO-2-(2-PYRIDINYL)ETHYL]AMINO}-2-OXO-1(2H)-PYRAZINYL)-N-[(2-FLUORO-6-PYRIDINYL)METHYL]ACETAMIDE
ChEMBLCHEMBL141889
DrugBankDB07548
ZINCZINC000000602992
PDB chain1mu6 Chain B Residue 248 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1mu6 Metabolism-directed optimization of 3-aminopyrazinone acetamide thrombin inhibitors. Development of an orally bioavailable series containing P1 and P3 pyridines.
Resolution1.99 Å
Binding residue
(original residue number in PDB)		H57 Y60A N98 L99 A190 C191 S195 S214 W215 G216
Binding residue
(residue number reindexed from 1)		H43 Y47 N95 L96 A192 C193 S197 S218 W219 G220
Annotation score1
Binding affinityMOAD: Ki=4.2nM
PDBbind-CN: -logKd/Ki=8.38,Ki=4.2nM
BindingDB: Ki=4.2nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 E192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H43 D99 E194 G195 D196 S197 G198
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:1mu6, PDBe:1mu6, PDBj:1mu6
PDBsum1mu6
PubMed12570369
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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