Only a few agonists exhibit selectivity between the AMPA and the kainate subtypes of the glutamate receptor. The most commonly used kainate receptor preferring agonist, (S)-2-amino-3-(5-tert-butyl-3-hydroxy-4-isoxazolyl)propionic acid [(S)-ATPA], is an (R,S)-2-amino-3-(5-methyl-3-hydroxy-4-isoxazolyl)propionic acid (AMPA) derivative in which the methyl group at the 5-position of the isoxazole ring has been replaced by a tertbutyl group. When characterized by the two-electrode voltage clamp method in Xenopus laevis oocytes, ATPA exhibits at least 50-fold higher potency on the kainate receptor subtype, GluR5, compared with the AMPA receptors. Through mutagenesis studies of GluR5 and the AMPA receptor subtype, GluR1, we demonstrate that this pronounced selectivity for ATPA can be ascribed to Ser741 in GluR5 and Met722 in GluR1. Examination of other aliphatic substitutions at the 5-position of the isoxazole ring revealed that (R,S)-2-amino-3-(5-isopropyl-3-hydroxy-4-isoxazolyl)propionic acid (isopropyl-AMPA) displayed a 6-fold higher potency for GluR5 than for GluR1, whereas the analogs, propyl-AMPA and isobutyl-AMPA, did not exhibit significantly different potencies. Our study suggests that the GluR5 selectivity was a result not only of steric interference between the bulky tert-butyl group in ATPA and the methionine (Met722) in GluR1 but also a serine-dependent stabilization of the active conformation of GluR5 induced by ATPA. The stabilization was agonist-dependent and observed only for ATPA and isopropyl-AMPA, not for other AMPA analogs with bulky substitutions at the 5-position of the isoxazole ring.