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The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures

Figure 4

Overlapping binding sites suggest structural mechanisms for observed small molecule effects.

(A) Sanglifehrin (cyan, PDB 1NMK:SFM) binds to cyclophilin A (grey, 1NMK; orange, 1AK4:A) at the same position that binds the HIV Gag capsid protein (purple, 1AK4:D). (B) Fusicoccin (cyan, 1O9E:FSC) binds to a region of the plant 14-3-3 protein (grey, 1O9E) that is homologous to the 14-3-3- (orange, 1A38:A) binding site for phosphopeptides (purple, 1A38:P). (C) Bepridil (cyan and blue, 1LXF:BEP) binds to Troponin C (grey, 1LXF:C) at positions that are homologous to the calmodulin (orange, 1K93:D) interface for anthrax edema factor (purple, 1K93:A). Troponin C aligns to both EF-hand motifs in calmodulin: The binding site aligned with EF-motif 2 (cyan) exhibits greater overlap with the anthrax edema factor interface than EF-motif 1 (blue).

Figure 4