Given the importance of G-protein-coupled receptors as pharmacological targets in medicine, efforts directed at the understanding the molecular mechanism by which pharmacological compounds regulate their activity is of paramount importance. Here, we investigated at an atomic level the mechanism of inverse agonism and partial agonism of two high affinity, high selectivity very similar non-peptide ligands of the cholecystokinin-2 receptor (CCK2R) which differ by the absence or presence of a methyl group on their indole moiety. Using in silico, site-directed mutagenesis and pharmacological experiments, we demonstrated that these functionally different activities are due to differing anchoring modes of the two compounds to a residue of helix II (Thr-2.61) in the inactive state of the CCK2R. The binding mode of the inverse agonist allows the ligand to interact through its phenyl moiety with a key amino acid for CCK2R activation (Trp-6.48), preventing rotation of helix VI and, thus, CCK2R activation, whereas the partial agonist binds deeper into the binding pocket and closer to helix V, so that CCK2R activation is favored. This study on the molecular mechanism of ligand action opens the possibility of target-based optimization of G protein-coupled receptor non-peptide ligands.G protein-coupled receptors (GPCRs) 3 are membrane-embedded proteins having seven transmembrane domains, responsible for communication between the cell and its environment (1). GPCRs represent, therefore, a major focus in functional genomics programs and drug development research (2).GPCRs naturally exist in different conformations which correspond to both active and inactive states. Depending on their propensity to bind preferentially with one of these receptor conformations or to identically interact with both, synthetic ligands can behave as agonists, inverse agonists, or neutral antagonists. To date, three three-dimensional GPCR structures have been precisely determined by x-ray crystallography, namely that of rhodopsin and 2-and 1-adrenergic receptors (3-6). In this context, refinement of modeled GPCR structures in both active and inactive conformations and progress in the understanding of the precise mechanisms, which govern their activation, are of paramount importance for drug design strategies (7).The cholecystokinin-2 (CCK-2) receptor (CCK2R) belongs to family A of rhodopsin-like GPCRs. It binds both cholecystokinin and gastrin with a similar, high affinity (8, 9). CCK2R mediates a wide spectrum of CCK-and gastrininduced biological effects in the central nervous system and in periphery including anxiety, pain perception, and gastric acid secretion as well as controlling growth and differentiation of the gastric mucosa. The CCK2R and/or a constitutively active variant of this receptor may contribute to human diseases (10, 11). This has recently generated considerable interest in the identification, among the large panel of synthetic ligands, of CCK2R antagonists having an inverse agonist activity (12,13).The CCK2R appears to be an ex...