Metastin, also known as KiSS-1, the cognate ligand for the metastin receptor GPR54, is a peptide known to dramatically reduce metastasis in experimental models. Despite this, there is no reported structure for metastin nor any small molecule modulators of metastin function that could be used either clinically or experimentally. Here we report the NMR solution structure of a 13-residue metastin peptide in a membrane-like environment (SDS micelles) and find it to have a relatively stable helix conformation from residues 7 to 13. In assays for metastin receptor binding and calcium flux with receptor-transfected HEK-293 cells, we demonstrate through alanine scanning and amino acid substitutions that the peptide C-terminus shows helix periodicity in an NMR structural model and that Phe9, Arg12, and Phe13 are crucial to the activity of the peptide. These three residues lie on one face of the helix and define a pharmacophore site for metastin. We used these pharmacophore features in small molecule database searches to identify hits with submicromolar affinity for the metastin receptor. We also show here that molecules mimicking key elements of this pharmacophore site bind to the metastin receptor and act as full agonists, albeit with reduced potency compared to that of metastin itself. Together this structure-activity approach may yield pharmacologically useful compounds relevant in defining and modulating metastin receptor function.