Prediction of 5-HT3 receptor agonist-binding residues using homology modeling

5-HT3 receptors demonstrate significant structural and functional homology to other members of the Cys-loop ligand-gated ion channel superfamily. The extracellular domains of these receptors share similar sequence homology (similar to20%) with Limnaea acetylcholine binding protein, for which an x-ray crystal structure is available. We used this structure as a template for computer-based homology modeling of the 5-HT3 receptor extracellular domain. AutoDock software was used to dock 5-HT into the putative 5-HT3 receptor ligand-binding site, resulting in seven alternative energetically favorable models. Residues located no more than 5 Angstrom from the docked 5-HT were identified for each model; of these, 12 were found to be common to all seven models with five others present in only certain models. Some docking models reflected the cation-pi interaction previously demonstrated for W183, and data from these and other studies were used to define our preferred models.