Although a crystal structure and a pharmacophore model are available for cytochrome P450 2C8, the role of protein flexibility and specific ligand-protein interactions that govern substrate binding are poorly understood. X-ray crystal structures of P450 2C8 complexed with montelukast (2.8 Å ), troglitazone (2.7 Å ), felodipine (2.3 Å ), and 9-cis-retinoic acid (2.6 Å ) were determined to examine ligand-protein interactions for these chemically diverse compounds. Montelukast is a relatively large anionic inhibitor that exhibits a tripartite structure and complements the size and shape of the active-site cavity. The inhibitor troglitazone occupies the upper portion of the active-site cavity, leaving a substantial part of the cavity unoccupied. The smaller neutral felodipine molecule is sequestered with its dichlorophenyl group positioned close to the heme iron, and water molecules fill the distal portion of the cavity. The structure of the 9-cis-retinoic acid complex reveals that two substrate molecules bind simultaneously in the active site of P450 2C8. A second molecule of 9-cis-retinoic acid is located above the proximal molecule and can restrain the position of the latter for more efficient oxygenation. Solution binding studies do not discriminate between cooperative and noncooperative models for multiple substrate binding. The complexes with structurally distinct ligands further demonstrate the conformational adaptability of active site-constituting residues, especially Arg-241, that can reorient in the active-site cavity to stabilize a negatively charged functional group and define two spatially distinct binding sites for anionic moieties of substrates.Cytochrome P450 2C8 is one of the principal drug-metabolizing P450 4 monooxygenases expressed in human liver. It is the predominant hepatic P450 catalyzing the 6␣-hydroxylation of paclitaxel (1) and the epoxidation of arachidonic acid (2, 3). Additionally, P450 2C8 contributes extensively to the metabolism of drugs such as pioglitazone, rosiglitazone, troglitazone, amodiaquine, amiodarone, and cerivastatin (4) as well as to the oxidation of retinoic acid (5-8). A screen of 209 commonly used drugs and related compounds identified several potent inhibitors of P450 2C8, including montelukast, candesartan cilexetil, mometasone furoate, clotrimazole, and felodipine (9). In addition, the glucuronide of gemfibrozil is a potent inhibitor of P450 2C8 (10, 11), and this inhibition is thought to underlie a drug-drug interaction between gemfibrozil and cerivastatin that can increase risk of rhabdomyolysis. Interestingly, glucuronides of 17-estradiol (12) and diclofenac (13) are also P450 2C8 substrates.A pharmacophore model for substrates of P450 2C8 was proposed by Mansuy and co-workers (14) based on the observation that many substrates are large organic anions at physiologic pH and exhibit sites of oxidation that are located ϳ13 Å from the anionic group. Additionally, it was noted that several polar moieties are often present at intermediate distances between the site o...