An In Silico Analysis of the Binding Modes and Binding Affinities of Small Molecule Modulators of PDZ-Peptide Interactions
Figure 3
Differences between PDZ2 and PDZ3 of PSD-95.
(A) Local alignment of the sequences of 2nd (PDB ID: 1QLC) and 3rd (PDB ID: 1BE9) PDZ domains of PSD-95 protein by BLAST and the conservation of the binding pocket residues is highlighted. (B) Ribbon diagrams depicting the structures 1BE9 and 1QLC. Regions in both 1BE9 and 1QLC, which show alignment in Figure 3A, are colored in cyan, while the N- and C-terminus residues, which did not align, are depicted in magenta. The longer loop region in 1QLC corresponding to the insertion seen in the local alignment is colored in purple. The binding pocket residues made flexible during docking are shown in red color. (C) Schematic depiction of the grid box used for docking of ligands on both PDZ domains. The dimension are x = 38Å, y = 74Å & z = 34Å.