Figure 4: In silico docking of compound 1 into the PPARγ binding pocket. | Scientific Reports

Figure 4: In silico docking of compound 1 into the PPARγ binding pocket.

From: A compound-based proteomic approach discloses 15-ketoatractyligenin methyl ester as a new PPARγ partial agonist with anti-proliferative ability

Figure 4

(a) Binding mode of compound 1 (yellow sticks) into the PPARγ binding site represented as a blue marine ribbon model. Only amino acids located within 4 Å of the bound ligand are displayed (white sticks) and labelled. The Ω-loop, a flexible loop region between H2′ and H3, and the β sheet region of the LBD, are displayed. H-bonds discussed in the text are depicted as dashed black lines. The 2D ligand-interaction diagram of 1 is depicted in panel (b). Positively charged amino acids are represented with dark blue circles, polar amino acids are represented with light blue circles and hydrophobic amino acids are represented with green circles. Hydrogen bonds are depicted with purple arrows–dashed arrows for H-bonds involving amino acid side chain and regular arrows for H-bonds involving amino acid backbone. (c) Cα superposition of the complexes of PPARγ with compound 1 and Rosiglitazone (green sticks, PDB code 2PRG).

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