Structure of PDB 3c27 Chain B Binding Site BS03

Receptor Information
>3c27 Chain B (length=249) 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
FVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
Ligand information
Ligand IDDKK
InChIInChI=1S/C19H20F3N7O2/c20-17-13(9-16(30)27-7-8-31-29-18(24)25)12(10-23)4-5-14(17)28-11-19(21,22)15-3-1-2-6-26-15/h1-6,28H,7-9,11H2,(H,27,30)(H4,24,25,29)
InChIKeySTHCHQXQLDMISY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=N)NOCCNC(=O)Cc1c(F)c(NCC(F)(F)c2ccccn2)ccc1C#N
ACDLabs 10.04FC(F)(c1ncccc1)CNc2ccc(C#N)c(c2F)CC(=O)NCCONC(=[N@H])N
OpenEye OEToolkits 1.5.0[H]N=C(N)NOCCNC(=O)Cc1c(ccc(c1F)NCC(c2ccccn2)(F)F)C#N
OpenEye OEToolkits 1.5.0[H]/N=C(\N)/NOCCNC(=O)Cc1c(ccc(c1F)NCC(c2ccccn2)(F)F)C#N
FormulaC19 H20 F3 N7 O2
NameN-[2-(carbamimidamidooxy)ethyl]-2-{6-cyano-3-[(2,2-difluoro-2-pyridin-2-ylethyl)amino]-2-fluorophenyl}acetamide
ChEMBLCHEMBL257543
DrugBankDB07665
ZINCZINC000029042456
PDB chain3c27 Chain B Residue 5000 [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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PDB3c27 Cyanofluorophenylacetamides as Orally Efficacious Thrombin Inhibitors
Resolution2.182 Å
Binding residue
(original residue number in PDB)		H79 Y83 W86 L132 D229 A230 S235 S256 W257 G258
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 L96 D191 A192 S197 S218 W219 G220
Annotation score1
Binding affinityBindingDB: Ki=1.2nM
Enzymatic activity
Catalytic site (original residue number in PDB) H79 D135 E232 G233 D234 S235 G236
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:3c27, PDBe:3c27, PDBj:3c27
PDBsum3c27
PubMed
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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