Fig. 4: MDS revealed ligand-induced conformational ensembles of PPARγ-LBD.
From: Structural determinants of non-covalent PPARγ inverse agonism and their therapeutic implications
A Heatmap clustering analysis of per-residue MM/PBSA binding energy profiles across twenty-six SR10171 analogs based on their residue interaction profiles. Each row represents a ligand-bound complex, and each column corresponds to a residue within the LBD, annotated with secondary structural elements along the top. Color intensity reflects the total free energy contribution of each residue (blue = favorable, red = unfavorable). Structural overlay of representative binding poses of B SR10171, C SR10221, D Compound 2, and E Compound 23 within the PPARγ-LBD. Dashed lines indicate interatomic distances (Ǻ) between ligand atoms and key residues. F 3D-PCA of the dynamic cross-correlation matrices (DCCMs) derived from MDS. Each point represents a ligand-bound complex, color-coded by the functional classification (green: non-IA, blue: partial-IA, purple: full-IA).
