Structure of PDB 1gj5 Chain H Binding Site BS02

Receptor Information

>1gj5 Chain H (length=250) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF

Ligand information

• Ligand ID: 130
• InChI: InChI=1S/C20H16N4O/c21-19(22)13-9-10-16-17(11-13)24-20(23-16)15-8-4-7-14(18(15)25)12-5-2-1-3-6-12/h1-11,25H,(H3,21,22)(H,23,24)
• InChIKey: LMGQGPVCSYOMNS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: NC(=N)c1ccc2[nH]c(nc2c1)c3cccc(c3O)c4ccccc4
  OpenEye OEToolkits 1.5.0: [H]N=C(c1ccc2c(c1)nc([nH]2)c3cccc(c3O)c4ccccc4)N
  ACDLabs 10.04: Oc4c(c1ccccc1)cccc4c3nc2cc(ccc2n3)C(=[N@H])N
  OpenEye OEToolkits 1.5.0: [H]/N=C(\c1ccc2c(c1)nc([nH]2)c3cccc(c3O)c4ccccc4)/N
• Formula: C20 H16 N4 O
• Name: 2-(2-HYDROXY-BIPHENYL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE
• ChEMBL: CHEMBL327715
• DrugBank: DB01725
• ZINC: ZINC000002047577
• PDB chain: 1gj5 Chain H Residue 410

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1gj5 Engineering inhibitors highly selective for the S1 sites of Ser190 trypsin-like serine protease drug targets.
• Resolution: 1.73 Å
• Binding residue (original residue number in PDB): C42 H57 C58 W60D D189 A190 E192 S195 V213
• Binding residue (residue number reindexed from 1): C28 H43 C44 W50 D192 A193 E195 S198 V218
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=4.96,Ki=11uM

Enzymatic activity

• 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

External links

• PDB: RCSB:1gj5, PDBe:1gj5, PDBj:1gj5
• PDBsum: 1gj5
• PubMed: 11731301
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)