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

Figure 2

Ligand-protein binding site overlap observed at protein–protein interactions as a function of sequence identity.

The maximum observed ligand binding site overlap (y-axis) for (A) inter-molecular domain–domain and (B) domain–peptide interactions, as a function of the ligand binding site sequence identity (x-axis). The densities in these plots are represented by colors that range from yellow (no density) to blue (maximum density). The (C) maximal and (D) cumulative overlap profile is shown at a minimum ligand binding site identity threshold of 30% for inter-molecular (black), intra-molecular (orange) domain–domain, and domain–peptide (cyan) interactions. Tick marks indicate interfaces that exhibit a particular level of interface coverage. The overlap score refers to the fraction of interface residues aligned to ligand binding site residues (Eqn 2).

Figure 2

doi: https://doi.org/10.1371/journal.pcbi.1000668.g002