Structure of PDB 1ktt Chain B Binding Site BS03

Receptor Information
>1ktt Chain B (length=252) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
GE
Ligand information
Ligand IDC02
InChIInChI=1S/C22H21N5O2S/c1-27-20-12-11-17(26-30(28,29)18-5-3-2-4-6-18)14-19(20)25-21(27)13-15-7-9-16(10-8-15)22(23)24/h2-12,14,26H,13H2,1H3,(H3,23,24)
InChIKeyMEUAVGJWGDPTLF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=S(=O)(c1ccccc1)Nc4ccc2c(nc(n2C)Cc3ccc(C(=[N@H])N)cc3)c4
OpenEye OEToolkits 1.5.0Cn1c2ccc(cc2nc1Cc3ccc(cc3)C(=N)N)NS(=O)(=O)c4ccccc4
CACTVS 3.341Cn1c(Cc2ccc(cc2)C(N)=N)nc3cc(N[S](=O)(=O)c4ccccc4)ccc13
FormulaC22 H21 N5 O2 S
Name4-(5-BENZENESULFONYLAMINO-1-METHYL-1H-BENZOIMIDAZOL-2-YLMETHYL)-BENZAMIDINE
ChEMBLCHEMBL46780
DrugBankDB07508
ZINCZINC000002043397
PDB chain1ktt Chain B Residue 1 [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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PDB1ktt Structure-based design of novel potent nonpeptide thrombin inhibitors.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D E97A N98 L99 I174 D189 A190 V213 S214 W215 G216 G219 C220
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 E94 N95 L96 I172 D192 A193 V218 S219 W220 G221 G223 C224
Annotation score1
Binding affinityMOAD: ic50=1.5uM
PDBbind-CN: -logKd/Ki=5.82,IC50=1.5uM
BindingDB: IC50=1500nM
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 E195 G196 D197 S198 G199
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:1ktt, PDBe:1ktt, PDBj:1ktt
PDBsum1ktt
PubMed11960487
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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