Fig. 3
Chemical definition of compound 484 interaction with HIV-1 Env. a Comparison of cocrystal structure of 484 with docking simulation. The two structures are superimposed by the gp120 (484 not used for superimposition). Simulated 484 complex structure is colored in black and co-crystal structure colored in orange (lower left). 2Fo-Fc electron density showing the 484 binding pocket is contoured at 2σ (top right). b Location of the entry inhibitor binding pocket in the context of HIV-1 Env trimer. The black square indicates the location of the inhibitor binding pocket. Three main protein segments interacting with the inhibitors are highlighted in cyan, magenta and green for residues 107–117, 369–385 and 423–436 respectively. c Detailed view of the 484 binding site. Upper panel on the left shows the residues of the β20−β21 hairpin (green fragment) interacting with 484. Lower panel on the left shows the all other residues interacting with 484 (excluding residues on the β20−β21 hairpin, which is removed for clarity). Right, the 484-Env interaction is shown as a 2D plot, with residues belonging to different major segments highlighted in different shades. Hydrophobic interactions are shown as sunray symbols while hydrophilic interactions are shown as dotted lines
