Fig. 4: Binding poses of the designed ligands.
From: Chemical manipulation of an activation/inhibition switch in the nuclear receptor PXR
a–d Crystal structures of PXR LBD complexed with SJPYT-312, SJPYT-326, SJPYT-328, or SJPYT-331. Region B moieties bind to the π-trap (violet) and leucine cage (orange), and region A groups are oriented toward α12 (dark red). The 4-methoxy groups (region A) of agonists SJPYT-326 and SJPYT-328 interact with the α12 cleft (spheres), and this interaction is absent in the antagonists SJPYT-312 and SJPYT-331 (dashed circles). e Overlay of PXR LBD bound to SJPYT-312 or SJPYT-331. SJPYT-331 binds tightly to the π-trap. f Overlay of PXR LBD bound to SJPYT-310, SJPYT-312, SJPYT-331, SJPYT-326, SJPYT-328, or SJB7. All antagonist structures are shown in gray, and all agonist structures are shown in purple. When antagonist is bound, PXR L428 shifts away from SRC-1 L690. g The distances between the closest atoms of PXR L428 and SRC-1 L690 were calculated for the indicated complexes. The measurements were taken for both chains of each structure, and lines represent the mean values. Source data for (g) are provided as a Source Data file.
