Distinct inactive conformations of the dopamine D2 and D3 receptors correspond to different extents of inverse agonism.

By analyzing and simulating inactive conformations of the highly-homologous dopamine D and D receptors (DR and DR), we find that eticlopride binds DR in a pose very similar to that in the DR/eticlopride structure but incompatible with the DR/risperidone structure. In addition, risperidone occupies a sub-pocket near the Na binding site, whereas eticlopride does not. Based on these findings and our experimental results, we propose that the divergent receptor conformations stabilized by Na-sensitive eticlopride and Na-insensitive risperidone correspond to different degrees of inverse agonism. Moreover, our simulations reveal that the extracellular loops are highly dynamic, with spontaneous transitions of extracellular loop 2 from the helical conformation in the DR/risperidone structure to an extended conformation similar to that in the DR/eticlopride structure. Our results reveal previously unappreciated diversity and dynamics in the inactive conformations of DR. These findings are critical for rational drug discovery, as limiting a virtual screen to a single conformation will miss relevant ligands.