Fig. 4.

The second binding pocket defined by R-22 is differentially modulated by non-conserved residues in D3R and D2R. (A) In addition to the core binding pocket, which essentially overlaps with that of eticlopride, the potential docking conformations of the core-constrained (see Supplementary information) D3R-selective compound R-22 position the extended aryl amide within a second binding pocket comprised by the junction of ECL1 and ECL2 and the interface of helices II, VII and I (dotted orange ellipse in A). (B) In the docking pose with the most extended conformation of R-22 (yellow), the ligand makes contact with several key conserved residues, including Asp110^3.32, Tyr373^7.43 and Glu90^2.65. The linker region of R-22 connecting the aryl amide and phenylpiperazine moieties (see fig. S1) is in a thinner representation. The 2,3-diCl-phenylpiperazine occupies essentially the same space as bound eticlopride (orange). (C–D) Close-up view of the interface of helices II, VII, and I of the D3R (C) and D2R (D) showing the results of molecular dynamics simulations indicating that the non-conserved regions of helix I and position 7.38 (orange) may orient key conserved contact residues differently and alter the shape of the second binding pocket, as reflected by the simulated distances between Glu90^2.65 and Tyr373^7.43 in D3R (cyan) and D2R (magenta) (see fig. S7).