Structure of PDB 2bdy Chain A Binding Site BS02

Receptor Information
>2bdy Chain A (length=276) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADCGLRPLFEKKSLEDKTERELLESYIIVEGSDAEIGMSPWQVMLFRKSP
QELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYER
NIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDR
ETAASLLQAGYKGRVTGWGNLKETGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEG
CDRDGKYGFYTHVFRLKKWIQKVIDQ
Ligand information
Ligand IDUNB
InChIInChI=1S/C27H26N4O4S/c1-17-9-14-23(31-36(34,35)24-8-4-6-19-5-2-3-7-21(19)24)26(33)22(17)15-25(32)30-16-18-10-12-20(13-11-18)27(28)29/h2-14,31,33H,15-16H2,1H3,(H3,28,29)(H,30,32)
InChIKeyKWJVADNYZMUTJY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=S(=O)(Nc1ccc(c(c1O)CC(=O)NCc2ccc(C(=[N@H])N)cc2)C)c4c3ccccc3ccc4
OpenEye OEToolkits 1.5.0[H]N=C(c1ccc(cc1)CNC(=O)Cc2c(ccc(c2O)NS(=O)(=O)c3cccc4c3cccc4)C)N
OpenEye OEToolkits 1.5.0[H]/N=C(\c1ccc(cc1)CNC(=O)Cc2c(ccc(c2O)NS(=O)(=O)c3cccc4c3cccc4)C)/N
CACTVS 3.341Cc1ccc(N[S](=O)(=O)c2cccc3ccccc23)c(O)c1CC(=O)NCc4ccc(cc4)C(N)=N
FormulaC27 H26 N4 O4 S
NameN-(4-CARBAMIMIDOYL-BENZYL)-2-[2-HYDROXY-6-METHYL-3-(NAPHTHALENE-1-SULFONYLAMINO)-PHENYL]-ACETAMIDE
ChEMBLCHEMBL1196664
DrugBank
ZINCZINC000016051814
PDB chain2bdy Chain A Residue 401 [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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PDB2bdy Phenolic P2/P3 core motif as thrombin inhibitors--design, synthesis, and X-ray co-crystal structure.
Resolution1.61 Å
Binding residue
(original residue number in PDB)		H79 Y83 W86 E130 L132 I209 D229 A230 C231 S235 V255 S256 W257 G258 G260
Binding residue
(residue number reindexed from 1)		H70 Y74 W77 E121 L123 I199 D219 A220 C221 S225 V245 S246 W247 G248 G250
Annotation score1
Binding affinityMOAD: ic50=0.017uM
PDBbind-CN: -logKd/Ki=7.77,IC50=17nM
BindingDB: IC50=17nM
Enzymatic activity
Catalytic site (original residue number in PDB) H79 D135 E232 G233 D234 S235 G236
Catalytic site (residue number reindexed from 1) H70 D126 E222 G223 D224 S225 G226
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
Cellular Component
GO:0005576 extracellular region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2bdy, PDBe:2bdy, PDBj:2bdy
PDBsum2bdy
PubMed16290930
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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