Structure of PDB 2c8w Chain B Binding Site BS03

Receptor Information
>2c8w 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 IDC7M
InChIInChI=1S/C25H29ClN6O4S/c1-36-21-8-10-22(11-9-21)37(34,35)29-16-25(33)23(13-18-5-3-2-4-6-18)27-15-19-14-20(26)7-12-24(19)32-17-28-30-31-32/h2-12,14,17,23,25,27,29-31,33H,13,15-16H2,1H3/p+1/t23-,25+/m0/s1
InChIKeyLMFQPEFBZUDVPR-UKILVPOCSA-O
SMILES
SoftwareSMILES
CACTVS 3.341COc1ccc(cc1)[S](=O)(=O)NC[C@@H](O)[C@H](Cc2ccccc2)[NH2+]Cc3cc(Cl)ccc3N4NNN=C4
ACDLabs 10.04O=S(=O)(c1ccc(OC)cc1)NCC(O)C(Cc2ccccc2)[NH2+]Cc3cc(Cl)ccc3N4C=NNN4
OpenEye OEToolkits 1.5.0COc1ccc(cc1)S(=O)(=O)NCC(C(Cc2ccccc2)[NH2+]Cc3cc(ccc3N4C=NNN4)Cl)O
OpenEye OEToolkits 1.5.0COc1ccc(cc1)S(=O)(=O)NC[C@H]([C@H](Cc2ccccc2)[NH2+]Cc3cc(ccc3N4C=NNN4)Cl)O
CACTVS 3.341COc1ccc(cc1)[S](=O)(=O)NC[CH](O)[CH](Cc2ccccc2)[NH2+]Cc3cc(Cl)ccc3N4NNN=C4
FormulaC25 H30 Cl N6 O4 S
Name(2S,3R)-N-[5-CHLORO-2-(2,3-DIHYDRO-1H-TETRAZOL-1-YL)BENZYL]-3-HYDROXY-4-{[(4-METHOXYPHENYL)SULFONYL]AMINO}-1-PHENYLBUTA N-2-AMINIUM;
INHIBITOR OF THROMBIN
ChEMBL
DrugBank
ZINC
PDB chain2c8w Chain B Residue 1249 [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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PDB2c8w Application of Fragment Screening and Fragment Linking to the Discovery of Novel Thrombin Inhibitors
Resolution1.96 Å
Binding residue
(original residue number in PDB)
H57 Y60A W60D E97A N98 L99 A190 C191 E192 V213 W215 G216 G219 C220 G226 F227
Binding residue
(residue number reindexed from 1)
H43 Y47 W50 E94 N95 L96 A192 C193 E194 V217 W219 G220 G222 C223 G230 F231
Annotation score1
Binding affinityMOAD: ic50=3.7nM
PDBbind-CN: -logKd/Ki=8.43,IC50=3.7nM
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:2c8w, PDBe:2c8w, PDBj:2c8w
PDBsum2c8w
PubMed16480269
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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