Structure of PDB 1mue Chain B Binding Site BS03

Receptor Information
>1mue 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 IDCDD
InChIInChI=1S/C20H17ClF3N5O3/c21-16-10-26-18(27-12-20(23,24)15-7-3-4-8-29(15)32)19(31)28(16)11-17(30)25-9-13-5-1-2-6-14(13)22/h1-8,10H,9,11-12H2,(H,25,30)(H,26,27)
InChIKeyZIGSBBKEPNQXRG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04Fc1ccccc1CNC(=O)CN3C(Cl)=CN=C(NCC(F)(F)c2[n+]([O-])cccc2)C3=O
OpenEye OEToolkits 1.5.0c1ccc(c(c1)CNC(=O)CN2C(=CN=C(C2=O)NCC(c3cccc[n+]3[O-])(F)F)Cl)F
CACTVS 3.341[O-][n+]1ccccc1C(F)(F)CNC2=NC=C(Cl)N(CC(=O)NCc3ccccc3F)C2=O
FormulaC20 H17 Cl F3 N5 O3
Name2-(6-CHLORO-3-{[2,2-DIFLUORO-2-(1-OXIDO-2-PYRIDINYL)ETHYL]AMINO}-2-OXO-1(2H)-PYRAZINYL)-N-[(2-FLUOROPHENYL)METHYL]ACETAMIDE
ChEMBLCHEMBL282837
DrugBankDB07550
ZINCZINC000000591438
PDB chain1mue 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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PDB1mue Pharmacokinetic optimization of 3-amino-6-chloropyrazinone acetamide thrombin inhibitors. Implementation of P3 pyridine N-oxides to deliver an orally bioavailable series containing P1 N-benzylamides.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		H57 Y60A L99 A190 S195 S214 W215 G216
Binding residue
(residue number reindexed from 1)		H43 Y47 L96 A192 S197 S218 W219 G220
Annotation score1
Binding affinityMOAD: Ki=2.3nM
PDBbind-CN: -logKd/Ki=8.64,Ki=2.3nM
BindingDB: Ki=2.3nM
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:1mue, PDBe:1mue, PDBj:1mue
PDBsum1mue
PubMed12657281
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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