Skip to main content
. Author manuscript; available in PMC: 2014 Oct 7.
Published in final edited form as: Nat Commun. 2014 Apr 7;5:3571. doi: 10.1038/ncomms4571

Figure 9. Alternate site-bound ligands uniquely protrude around helix 3 to affect the conformation of the Ω loop.

Figure 9

Ligands bound deep in the canonical LBP are colored orange, and the second bound ligand, whether it occupies the alternate site region or not, are colored blue; Ω loop region, if observed in the crystal structure, from M257-V277 is colored green. Alternate site bound ligands that affect the Ω loop conformation are also circled. (a) Co-crystal structure of the PPARγ LBD bound to one molecule of MRL20 (PDB: 2Q59). (b) Co-crystal structure of the PPARγ LBD bound to one molecule of T2384 (PDB: 3K8S; chain A). (c) Co-crystal structure of the PPARγ LBD with MRL20 (orange) (PDB: 2Q59) docked with a second MRL20 ligand (blue). (d) Co-crystal structure of the PPARγ LBD bound to two molecules of T2384 in the canonical LBP (orange) and alternate site (blue) (PDB: 3K8S; chain B). (e) Co-crystal structure of the PPARγ LBD bound to two molecules of 9-(S)-HODE (PDB: 2VSR). (f) Co-crystal structure of the PPARγ LBD bound to 5-methoxy-indole acetate (orange) and 15-oxoETE (blue) (PDB: 3ADW).