Probing ligand binding modes of human cytochrome P450 2J2 by homology modeling, molecular dynamics simulation, and flexible molecular docking

Proteins. 2008 May 1;71(2):938-49. doi: 10.1002/prot.21778.


Cytochrome P450 (P450) 2J2 catalyzes epoxidation of arachidonic acid to eicosatrienoic acids, which are related to a variety of diseases such as coronary artery disease, hypertension, and carcinogenesis. Recent experimental data also suggest that P450 2J2 could be a novel biomarker and a potential target for cancer therapy. However, the active site topology and substrate specificity of this enzyme remain unclear. In this study, a three-dimensional model of human P450 2J2 was first constructed on the basis of the crystal structure of human P450 2C9 in complex with a substrate using homology modeling method, and refined by molecular dynamics simulation. Flexible docking approaches were then employed to dock four ligands into the active site of P450 2J2 in order to probe the ligand-binding modes. By analyzing the results, active site architecture and certain key residues responsible for substrate specificity were identified on the enzyme, which might be very helpful for understanding the enzyme's biological role and providing insights for designing novel inhibitors of P450 2J2.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Butyrophenones / chemistry
  • Computer Simulation
  • Cytochrome P-450 CYP2J2
  • Cytochrome P-450 Enzyme Inhibitors
  • Cytochrome P-450 Enzyme System / chemistry*
  • Cytochrome P-450 Enzyme System / metabolism*
  • Drug Design
  • Humans
  • Ligands
  • Models, Molecular
  • Molecular Sequence Data
  • Oxygenases / antagonists & inhibitors
  • Oxygenases / chemistry*
  • Oxygenases / metabolism*
  • Piperidines / chemistry
  • Protein Interaction Domains and Motifs
  • Sequence Alignment
  • Structural Homology, Protein*
  • Substrate Specificity
  • Terfenadine / analogs & derivatives
  • Terfenadine / chemistry


  • Butyrophenones
  • CYP2J2 protein, human
  • Cytochrome P-450 Enzyme Inhibitors
  • Ligands
  • Piperidines
  • Terfenadine
  • Cytochrome P-450 Enzyme System
  • Oxygenases
  • Cytochrome P-450 CYP2J2
  • ebastine