Mapping of drug binding positions and binding pockets to HIV-1 gag protein monomers. The surface spectrum colors indicate the most to the least conserved positions in subtype B from blue CI = 0 to pink CI ≥ 0.1. (A) Secondary structures of 4 gag proteins and 2 spacer peptides, annotated with five drug binding pocket locations. Gag proteins in cartoon representation are colored olive for matrix, blue for capsid, yellow for nucleocapsid, grey for p6, gold for p1 and p2. Bound inhibitors are represented in green sticks. (B) Mapping of drug binding positions to a surface representation of gag structure, with front and back views. Hypothesized binding positions of bevirimat are also annotated; known drug binding positions are colored red. (C) Surface representation of gag conservation in HIV-1 subtype B (Figure S3 in Additional file 2 illustrates other subtypes). (D) Surface representations of five drug binding pockets in HIV-1 subtype B (Figure S2 in Additional file 2 shows other subtypes). Inhibitor names are annotated according to publication (Additional file 1: Table S1). PDB entries of gag proteins: matrix, 1HIW; capsid, 3NTE; p2, 1U57; nucleocapsid, 2M3Z; p6, 2C55. PDB data of capsid inhibitors: 2BUO, 2L6E, 2XDE, 4E91, 4E92, 2JPR and 4INB, each of which was superimposed to 3H4E using PDBs of 5 drug binding pockets: pocket 1, 2XDE; pocket 2, 4INB; pocket 3, 2BUO; pocket 4, 4E91; pocket 5, 2M3Z. PyMOL V1.5 (http://www.pymol.org/).