Glucagon-like peptide-1 (GLP-1) activates the GLP-1 receptor (GLP-1R), which belongs to family B of the G-protein-coupled receptors. We previously identified a selective small molecule ligand, compound 2, that acted as a full agonist and allosteric modulator of GLP-1R. In this study, the structurally related small molecule, compound 3, stimulated cAMP production from GLP-1R, but not from the homologous glucagon receptor (GluR). The receptor selectivity encouraged a chimeric receptor approach to identify domains important for compound 3-mediated activation of GLP-1R. A subsegment of the GLP-1R transmembrane domain containing TM2 to TM5 was sufficient to transfer compound 3 responsiveness to GluR. Therefore, divergent residues in this subsegment of GLP-1R and GluR are responsible for the receptor selectivity of compound 3. Functional analyses of other chimeric receptors suggested that the existence of a helix-helix interface between TM1 and TM7 is important for the compound 3 response. Furthermore, site-directed mutagenesis revealed that a Phe195-Leu substitution in TM2 and a Thr391-Ala substitution in TM7 increased and decreased the efficacy of compound 3 without disturbing the potency or efficacy of GLP-1. Collectively, differential effects of receptor mutations suggest that TM2 and/or TM7 are important for compound 3-mediated activation of GLP-1R.