Edited by Norma AllewellLiver receptor homolog 1 (NR5A2, LRH-1) is an orphan nuclear hormone receptor that regulates diverse biological processes, including metabolism, proliferation, and the resolution of endoplasmic reticulum stress. Although preclinical and cellular studies demonstrate that LRH-1 has great potential as a therapeutic target for metabolic diseases and cancer, development of LRH-1 modulators has been difficult. Recently, systematic modifications to one of the few known chemical scaffolds capable of activating LRH-1 failed to improve efficacy substantially. Moreover, mechanisms through which LRH-1 is activated by synthetic ligands are entirely unknown. Here, we use x-ray crystallography and other structural methods to explore conformational changes and receptor-ligand interactions associated with LRH-1 activation by a set of related agonists. Unlike phospholipid LRH-1 ligands, these agonists bind deep in the pocket and do not interact with residues near the mouth nor do they expand the pocket like phospholipids. Unexpectedly, two closely related agonists with similar efficacies (GSK8470 and RJW100) exhibit completely different binding modes. The dramatic repositioning is influenced by a differential ability to establish stable face-to-face --stacking with the LRH-1 residue His-390, as well as by a novel polar interaction mediated by the RJW100 hydroxyl group. The differing binding modes result in distinct mechanisms of action for the two agonists. Finally, we identify a network of conserved water molecules near the ligand-binding site that are important for activation by both agonists. This work reveals a previously unappreciated complexity associated with LRH-1 agonist development and offers insights into rational design strategies.Liver receptor homolog 1 (LRH-1; NR5A2) is a nuclear hormone receptor (NR) 3 that controls expression of a diverse set of genes important both in normal physiology and disease. In addition to a vital role during development (1, 2), LRH-1 regulates many genes related to metabolism, proliferation, and cell survival. In the liver, LRH-1 regulates bile acid biosynthesis (3) and reverse cholesterol transport (4, 5), affecting hepatic and circulating cholesterol levels. Glucose metabolism is also regulated by LRH-1 at several points, including GLUT-4-mediated transport (6) and glucose phosphorylation, the latter of which is essential for proper postprandial glucose sensing, flux through glycolysis and glycogenesis pathways, and de novo lipogenesis (7). LRH-1 is a key mediator of the cell stress response through control of genes involved in the hepatic acute phase response (8) and in the cytoprotective resolution of endoplasmic reticulum stress (9). Additionally, LRH-1 can be aberrantly overexpressed in certain cancers and can promote tumor growth through estrogen receptor and -catenin signaling (10 -16).Considering the breadth and significance of these physiological effects, LRH-1 modulators are highly desired as potential therapeutic agents. Chemical modulators would al...