Figure 1.

A) The crystallized HIV-1 protease uniquely bound by two identical inhibitors, with pose α colored in grey and pose β in black. B) The crystal structure 3BC4 with Damm compound 1¹² (black) bound at the eye site. C) The 5-Nitroindole fragment (black) crystallized in the eye site by Perryman et al.²⁸ D) A 2-dimensional representation of the pyrrolidine inhibitor that was co-crystallized with 3BC4. The affinity (Kⁱ) of the compound for HIVp was measured by Klebe and coworkers as 20μM (WT), 41μM (I50V), and 4.5μM (I84V).¹¹ For the following figures, we have used a convention of orienting the complex so that a naphthyl occupies the eye position on the right (ie. Monomer 2). We are labeling the monomers as “1” and “2” instead of “A” and “B” to avoid confusion with the α and β notation for the ligands.