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Structure of PDB 1mu8 Chain B Binding Site BS03

Receptor Information
>1mu8 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 IDCDB
InChIInChI=1S/C21H21F3N6O2/c1-13-6-8-25-15(18(13)22)10-27-17(31)11-30-14(2)9-28-19(20(30)32)29-12-21(23,24)16-5-3-4-7-26-16/h3-9H,10-12H2,1-2H3,(H,27,31)(H,28,29)/p+2
InChIKeyWOYBPRBUPLYTPY-UHFFFAOYSA-P
SMILES
SoftwareSMILES
CACTVS 3.341CC1=C[NH+]=C(NCC(F)(F)c2cccc[nH+]2)C(=O)N1CC(=O)NCc3nccc(C)c3F
OpenEye OEToolkits 1.5.0Cc1ccnc(c1F)CNC(=O)CN2C(=C[NH+]=C(C2=O)NCC(c3cccc[nH+]3)(F)F)C
ACDLabs 10.04O=C(NCc1nccc(c1F)C)CN2C(=C[NH+]=C(C2=O)NCC(F)(F)c3[nH+]cccc3)C
FormulaC21 H23 F3 N6 O2
Name2-(6-CHLORO-3-{[2,2-DIFLUORO-2-(2-PYRIDINYL)ETHYL]AMINO}-2-OXO-1(2H)-PYRAZINYL)-N-[(2-FLUORO-3-METHYL-6-PYRIDINYL)METHYL]ACETAMIDE
ChEMBL
DrugBankDB07549
ZINC
PDB chain1mu8 Chain B Residue 248 [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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PDB1mu8 Metabolism-directed optimization of 3-aminopyrazinone acetamide thrombin inhibitors. Development of an orally bioavailable series containing P1 and P3 pyridines.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		H57 Y60A N98 A190 S195 V213 S214 W215 G216
Binding residue
(residue number reindexed from 1)		H43 Y47 N95 A192 S197 V217 S218 W219 G220
Annotation score1
Binding affinityMOAD: Ki=1nM
PDBbind-CN: -logKd/Ki=9.00,Ki=1.0nM
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:1mu8, PDBe:1mu8, PDBj:1mu8
PDBsum1mu8
PubMed12570369
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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