Structure of PDB 6yhj Chain L Binding Site BS01

Receptor Information

>6yhj Chain L (length=33) Species: 9606 (Homo sapiens)

SGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Ligand information

• Ligand ID: OQZ
• InChI: InChI=1S/C19H22ClN3O2S/c20-17-9-8-14(26-17)12-22-18(24)16-7-4-10-23(16)19(25)15(21)11-13-5-2-1-3-6-13/h1-3,5-6,8-9,15-16H,4,7,10-12,21H2,(H,22,24)/t15-,16+/m1/s1
• InChIKey: RAMUDOPEEQUPEA-CVEARBPZSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3ccc(s3)Cl)N
  OpenEye OEToolkits 2.0.7: c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NCc3ccc(s3)Cl)N
  CACTVS 3.385: N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCc3sc(Cl)cc3
  CACTVS 3.385: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3sc(Cl)cc3
• Formula: C19 H22 Cl N3 O2 S
• Name: (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-chloranylthiophen-2-yl)methyl]pyrrolidine-2-carboxamide
• PDB chain: 6yhj Chain H Residue 305

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6yhj Thrombin in complex with D-Phe-Pro-2-chlorothiophen derivative (16e)
• Resolution: 1.44 Å
• Binding residue (original residue number in PDB): S-1 E1C
• Binding residue (residue number reindexed from 1): S1 E3
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.4.21.5: thrombin.

Gene Ontology

Molecular Function

• GO:0004252 serine-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis
• GO:0007596 blood coagulation

Cellular Component

• GO:0005576 extracellular region

External links

• PDB: RCSB:6yhj, PDBe:6yhj, PDBj:6yhj
• PDBsum: 6yhj
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)