Fig. 8.

Schematic representation of AhR ligand binding domain docked with agonists TCDD (A), 4-Me-indole (B), 6-Me-indole (C), and 7-MeO-indole (D). TCDD binds favorably to the pocket with several hydrophobic residues facilitating the interactions with the TCDD core. All indole-substituted agonists bind with a similar binding mode and have conserved arene or cation-pi interactions with the aromatic ring of indole and hydrogen bond interaction with the amine group. In addition, many aromatic and hydrophobic residues facilitate the binding of these molecules. All residues that lie within a 5 Å radius from the center of the binding pocket are listed and colored according to their amphiphilicity profile. The schematic legend details the nature of the interactions of agonists with the residues in the binding pocket. The images were generated using the ligand interactions module in the MOE program.