3ME6

Crystal structure of cytochrome 2B4 in complex with the anti-platelet drug clopidogrel

Summary for 3ME6

• Entry DOI: 10.2210/pdb3me6/pdb
• Related: 1PO5 1SUO 2BDM 2Q6N 3G5N 3G93 3KW4
• Descriptor: Cytochrome P450 2B4, PROTOPORPHYRIN IX CONTAINING FE, Clopidogrel, ... (4 entities in total)
• Functional Keywords: p450, cytochrome p450 2b4, monooxygenase, oxidoreductase, membrane protein, cyp 2b4, cyp lm2
• Biological source: Oryctolagus cuniculus (rabbit)
• Cellular location: Endoplasmic reticulum membrane; Peripheral membrane protein: P00178
• Total number of polymer chains: 4
• Total formula weight: 220429.56

Authors

Gay, S.C.,Roberts, A.G.,Maekawa, K.,Talakad, J.C.,Hong, W.X.,Zhang, Q.,Stout, C.D.,Halpert, J.R. (deposition date: 2010-03-31, release date: 2010-09-15, Last modification date: 2023-09-06)

Primary citation

Gay, S.C.,Roberts, A.G.,Maekawa, K.,Talakad, J.C.,Hong, W.X.,Zhang, Q.,Stout, C.D.,Halpert, J.R.
Structures of cytochrome P450 2B4 complexed with the antiplatelet drugs ticlopidine and clopidogrel.
Biochemistry, 49:8709-8720, 2010

PubMed Abstract: Prior X-ray crystal structures of rabbit cytochrome P450 2B4 (2B4) in complexes with various imidazoles have demonstrated markedly different enzyme conformations depending on the size of the inhibitor occupying the active site. In this study, structures of 2B4 were determined with the antiplatelet drugs clopidogrel and ticlopidine, which were expected to have greater freedom of movement in the binding pocket. Ticlopidine could be modeled into the electron density maps in two distinct orientations, both of which are consistent with metabolic data gathered with other mammalian P450 enzymes. Results of ligand docking and heme-induced NMR relaxation of drug protons showed that ticlopidine was preferentially oriented with the chlorophenyl group closest to the heme. Because of its stereocenter, clopidogrel was easier to fit in the electron density and exhibited a single orientation, which points the chlorophenyl ring toward the heme. The C(α) traces of both complexes aligned very well with each other and revealed a compact, closed structure that resembles the conformation observed in two previously determined 2B4 structures with the small molecule inhibitors 4-(4-chlorophenyl)imidazole and 1-(4-chlorophenyl)imidazole. The 2B4 active site is able to accommodate small ligands by moving only a small number of side chains, suggesting that ligand reorientation is energetically favored over protein conformational changes for binding of these similarly sized molecules. Adjusting both protein conformation and ligand orientation in the active site gives 2B4 the flexibility to bind to the widest range of molecules, while also being energetically favorable.

PubMed: 20815363
DOI: 10.1021/bi100914z

Experimental method

X-RAY DIFFRACTION (3.1 Å)