Homology modelling of CYP3A4 from the CYP2C5 crystallographic template: analysis of typical CYP3A4 substrate interactions

Xenobiotica. 2004 Jun;34(6):549-69. doi: 10.1080/00498250410001691325.

Abstract

1. The results of homology modelling of cytochrome P4503A4 (CYP3A4), which is a human enzyme of major importance for the Phase 1 metabolism of drug substrates, from the CYP2C5 crystal structure is reported. 2. The overall homology between the two protein sequences was generally good (46%) with 24% of amino acid residues being identical and a 22% similarity between matched pairs in the CYP3A4 and CYP2C5 aligned sequences, thus indicating that CYP2C5 represents a viable template for modelling CYP3A4 by homology. 3. The CYP3A4 model appears to show consistency with the reported findings from the extensive site-directed mutagenesis studies already published. 4. Typical CYP3A4 substrates, such as midazolam, testosterone, nifedipine and verapamil, are shown to fit the putative active site of the enzyme structure in a manner consistent with their known positions of metabolism.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Crystallography, X-Ray
  • Cytochrome P-450 CYP3A
  • Cytochrome P-450 Enzyme System / chemistry*
  • Cytochrome P-450 Enzyme System / metabolism*
  • Cytochrome P450 Family 2
  • Humans
  • Models, Molecular*
  • Molecular Sequence Data
  • Molecular Structure
  • Pharmaceutical Preparations / chemistry
  • Pharmaceutical Preparations / metabolism
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Steroid 21-Hydroxylase / chemistry*
  • Substrate Specificity

Substances

  • Pharmaceutical Preparations
  • Cytochrome P-450 Enzyme System
  • CYP2C5 protein, Oryctolagus cuniculus
  • CYP3A protein, human
  • Cytochrome P-450 CYP3A
  • Cytochrome P450 Family 2
  • Steroid 21-Hydroxylase
  • CYP3A4 protein, human