Structure of PDB 2c93 Chain B Binding Site BS03

Receptor Information
>2c93 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 IDC4M
InChIInChI=1S/C20H28N2O4S/c1-13-10-19(26-4)14(2)15(3)20(13)27(24,25)22-12-18(23)17(21)11-16-8-6-5-7-9-16/h5-10,17-18,22-23H,11-12,21H2,1-4H3/t17-,18+/m0/s1
InChIKeyHORGTFOBJRCVMO-ZWKOTPCHSA-N
SMILES
SoftwareSMILES
CACTVS 3.341COc1cc(C)c(c(C)c1C)[S](=O)(=O)NC[C@@H](O)[C@@H](N)Cc2ccccc2
OpenEye OEToolkits 1.5.0Cc1cc(c(c(c1S(=O)(=O)NCC(C(Cc2ccccc2)N)O)C)C)OC
OpenEye OEToolkits 1.5.0Cc1cc(c(c(c1S(=O)(=O)NC[C@H]([C@H](Cc2ccccc2)N)O)C)C)OC
CACTVS 3.341COc1cc(C)c(c(C)c1C)[S](=O)(=O)NC[CH](O)[CH](N)Cc2ccccc2
ACDLabs 10.04O=S(=O)(c1c(cc(OC)c(c1C)C)C)NCC(O)C(N)Cc2ccccc2
FormulaC20 H28 N2 O4 S
NameN-[(2R,3S)-3-AMINO-2-HYDROXY-4-PHENYLBUTYL]-4-METHOXY-2,3,6-TRIMETHYLBENZENESULFONAMIDE;
INHIBITOR OF THROMBIN
ChEMBLCHEMBL379692
DrugBankDB07527
ZINCZINC000013681953
PDB chain2c93 Chain B Residue 1251 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2c93 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 L99 E192 W215 G216
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 L96 E194 W219 G220
Annotation score1
Binding affinityMOAD: ic50=12uM
PDBbind-CN: -logKd/Ki=4.92,IC50=12uM
BindingDB: IC50=12000nM
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:2c93, PDBe:2c93, PDBj:2c93
PDBsum2c93
PubMed16480269
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

[Back to BioLiP]