Cytochrome P450 (CYP) 3A4 is the most promiscuous of the human CYP enzymes and
contributes to the metabolism of approximately 50% of marketed drugs. It is also
the isoform most often involved in unwanted drug-drug interactions. A better
understanding of the molecular mechanisms governing CYP3A4-ligand interaction
therefore would be of great importance to any drug discovery effort. Here, we
present crystal structures of human CYP3A4 in complex with two well
characterized drugs: ketoconazole and erythromycin. In contrast to previous
reports, the protein undergoes dramatic conformational changes upon ligand
binding with an increase in the active site volume by >80%. The structures
represent two distinct open conformations of CYP3A4 because ketoconazole and
erythromycin induce different types of coordinate shifts. The binding of two
molecules of ketoconazole to the CYP3A4 active site and the clear indication of
multiple binding modes for erythromycin has implications for the interpretation
of the atypical kinetic data often displayed by CYP3A4. The extreme flexibility
revealed by the present structures also challenges any attempt to apply
computational design tools without the support of relevant experimental data.
Figure 1.
Fig. 1. Chemical structures of ketoconazole (A) and
erythromycin (B).
Figure 3.
Fig. 3. Ketoconazole binding to CYP3A4. Ketoconazole
molecules are shown in orange stick representation. The heme
group is shown in magenta. Secondary structure and stick
representations of side chains within 4 Å from the ligands
are shown in green. The C-terminal loop (residues 464–498) was
omitted for clarity. A superposition of the ligand-free
structure (Protein Data Bank ID code 1TQN) is shown in gray. The
mesh represents a F[o] – F[c] difference map contoured at 4.5
calculated in the
absence of ligands by using the program AutoBUSTER (19).
calculated in the
absence of ligands by using the program AutoBUSTER (19).
