The motilin receptor belongs to a group of class I G proteincoupled receptors that also includes the growth hormone secretagogue and ghrelin receptors. These represent clinically useful targets for pharmacotherapy. Their potentially unique structures and the molecular basis of their binding are not yet clear. We previously reported the initial affinity labeling of a region within this receptor (a cyanogen bromide fragment extending from the first to the second extracellular loop) using a position 1 photolabile motilin analog. To extend our understanding of the molecular basis of motilin binding, we have developed an additional radioiodinatable motilin analog probe having site of covalent attachment in position 5. This was a full agonist that bound to the motilin receptor specifically and with high affinity, and that efficiently established a single covalent bond to its receptor. Sequential chemical and enzymatic cleavage of labeled wild-type and mutant motilin receptor constructs established that the region of labeling was within the third extracellular loop. This was further localized to Phe 332 using radiochemical Edman degradation sequencing. These data provide the first spatial approximation constraint that can be used in the docking of this peptide ligand to its receptor. We hope that a series of such constraints can be determined to provide adequate structural information to begin to elucidate the conformation of this agonist-bound receptor and to ultimately be useful in the rational design of drugs acting at this important target.The detailed understanding of the basis for binding a ligand by a receptor can help refine our understanding of the conformation of the receptor and of the molecular basis for its activation. Although all members of the superfamily of guanine nucleotide-binding protein (G protein)-coupled receptors have structural similarities, with seven hydrophobic segments that are believed to traverse the plasma membrane, the details of even this most fundamental characteristic varies within the family of these receptors (Kolakowski, 1994;Ji et al., 1998). This superfamily is also remarkable for the structural diversity of the natural ligands that activate various members, with themes ranging from small photons and biogenic amines that bind within the confluence of transmembrane segments to larger peptide and glycoprotein ligands that bind to extracellular tail and loop domains.The class I G protein-coupled receptors that are activated by motilin and ghrelin were recognized only recently (Howard et al., 1996;McKee et al., 1997;Feighner et al., 1999) and cluster together in sequence analysis, having substantial structural similarity. This has typically been a predictor of similarity in ligand structure and mechanism of binding and activation (Kolakowski, 1994). Although these natural ligands have extensive sequence homology, ghrelin requires a unique post-translational modification for its activity that is not present or required for motilin (Kojima et al., 1999). This represents the N...