Molecular docking study of the interactions between the thioesterase domain of human fatty acid synthase and its ligands

Proteins. 2008 Mar;70(4):1228-34. doi: 10.1002/prot.21615.


Human fatty acid synthase (hFAS) thioesterase domain (TE) is an attractive drug target to treat obesity and cancer. On the basis of the recently published crystal structure of TE domain of hFAS, we performed molecular surface analysis and docking study to characterize the molecular interactions between the enzyme and its various ligands. Surface analysis identified the ligand-binding pocket of TE domain that encompasses the catalytic triad of Ser2308, His2481, Asp2338. Docking of palmitate, the main biological product of hFAS, into this pocket revealed the ligand-binding mode, in which the hydrophobic interactions are the dominant driving forces. The catalytic mechanism of TE domain can also be well explained based on the generated TE-palmitate complex structure. Moreover, the comparison of the binding modes of five fatty acids with chain lengths ranging from 12 to 20 carbons confirmed that the ligand binding pocket of TE domain is a decisive factor in chain length specificity. In addition, docking of two known TE inhibitors, c75 and orlistat revealed the pharmacophore of these hFAS TE inhibitors, which will prove useful in structure-based drug design against this important target.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Binding Sites
  • Catalytic Domain
  • Computer Simulation*
  • Fatty Acid Synthase, Type I / chemistry*
  • Humans
  • Ligands
  • Models, Molecular*
  • Palmitates
  • Protein Binding
  • Protein Structure, Tertiary


  • Ligands
  • Palmitates
  • FASN protein, human
  • Fatty Acid Synthase, Type I