Atazanavir, which is marketed as REYATAZ, is the first human immunodeficiency virus type 1 (HIV-1) protease inhibitor approved for once-daily administration. As previously reported, atazanavir offers improved inhibitory profiles against several common variants of HIV-1 protease over those of the other peptidomimetic inhibitors currently on the market. This work describes the X-ray crystal structures of complexes of atazanavir with two HIV-1 protease variants, namely, (i) an enzyme optimized for resistance to autolysis and oxidation, referred to as the cleavage-resistant mutant (CRM); and (ii) the M46I/V82F/I84V/L90M mutant of the CRM enzyme, which is resistant to all approved HIV-1 protease inhibitors, referred to as the inhibitor-resistant mutant. In these two complexes, atazanavir adopts distinct bound conformations in response to the V82F substitution, which may explain why this substitution, at least in isolation, has yet to be selected in vitro or in the clinic. Because of its nearly symmetrical chemical structure, atazanavir is able to make several analogous contacts with each monomer of the biological dimer.The human immunodeficiency virus type 1 (HIV-1) protease (PRT) enzyme is essential for viral replication. As such, it is an attractive target for antiviral therapy. Indeed, a sustained, international effort of structure-based drug design has led to the development of potent HIV-1 PRT inhibitors (PIs) that bind to the active site of mature PRT. Several of these drugs are currently in use for the treatment of AIDS (18,31,36). The seven FDA-approved PIs currently on the market (in order of approval [http://www.fda.gov/oashi/aids/virals.html])-saquinavir, ritonavir, indinavir, nelfinavir, amprenavir, lopinavir, and atazanavir-are competitive peptidomimetics (10,15). Unfortunately, the use of these PIs can lead to rapid selection for drug-resistant PRT variants (1,42,50). Mutations of the conserved PRT residues V82, I84, and L90 are among those most commonly observed in patients receiving PI-containing regimens. In addition, the collective data from clinical failures of antiviral therapy show considerable cross-resistance among the PIs (19). Both factors threaten the long-term effectiveness of these drugs. Therefore, it is important to understand the mechanisms that govern drug resistance in order to develop more effective inhibitors and to rationally formulate drug regimens.Atazanavir, a highly potent azapeptide, is the most recently approved HIV-1 PI. A favorable pharmacokinetic profile allows once-daily dosing (37,43,47). More importantly, atazanavir has a distinct resistance profile relative to those of the other approved PIs. Earlier in vitro studies demonstrated that the substitutions M46I, A71V, N88S, I84V, and I50L, which were identified in laboratory strains of PRT variants selected against atazanavir, may play important roles in the resistance phenotype and that multiple mutational pathways can lead to resistance (17). In clinical studies of treatment-experienced patients who received atazanavir-c...