Structure of PDB 2c8y Chain B Binding Site BS03

Receptor Information
>2c8y Chain B (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
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEGQPS
VLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGP
FVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
E
Ligand information
Ligand IDC3M
InChIInChI=1S/C20H22N2O3S/c21-19(12-15-6-2-1-3-7-15)20(23)14-22-26(24,25)18-11-10-16-8-4-5-9-17(16)13-18/h1-11,13,19-20,22-23H,12,14,21H2/t19-,20+/m0/s1
InChIKeyQSSWSEQPKCCATQ-VQTJNVASSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[C@@H](Cc1ccccc1)[C@H](O)CN[S](=O)(=O)c2ccc3ccccc3c2
OpenEye OEToolkits 1.5.0c1ccc(cc1)CC(C(CNS(=O)(=O)c2ccc3ccccc3c2)O)N
OpenEye OEToolkits 1.5.0c1ccc(cc1)C[C@@H]([C@@H](CNS(=O)(=O)c2ccc3ccccc3c2)O)N
CACTVS 3.341N[CH](Cc1ccccc1)[CH](O)CN[S](=O)(=O)c2ccc3ccccc3c2
ACDLabs 10.04O=S(=O)(c2cc1ccccc1cc2)NCC(O)C(N)Cc3ccccc3
FormulaC20 H22 N2 O3 S
NameN-[(2R,3S)-3-AMINO-2-HYDROXY-4-PHENYLBUTYL]NAPHTHALENE-2-SULFONAMIDE;
INHIBITOR OF THROMBIN
ChEMBLCHEMBL204086
DrugBankDB07522
ZINCZINC000013681950
PDB chain2c8y Chain B Residue 1252 [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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PDB2c8y Application of Fragment Screening and Fragment Linking to the Discovery of Novel Thrombin Inhibitors
Resolution2.2 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D N98 L99 W215 G216
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 N95 L96 W219 G220
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.00,IC50=100uM
BindingDB: IC50=100000nM
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:2c8y, PDBe:2c8y, PDBj:2c8y
PDBsum2c8y
PubMed16480269
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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