The cavity structure for docking the K+-competitive inhibitors in the gastric proton pump

2-Methyl-8-(phenylmethoxy) imidazo[1,2-a] pyridine-3-acetonitrile (SCH 28080) is a reversible inhibitor specific for the gastric proton pump. The inhibition pattern is competitive with K+. Here we studied the binding sites of this inhibitor on the putative three-dimensional structure of the gastric proton pump alpha-subunit that was constructed by homology modeling based on the structure of sarcoplasmic reticulum Ca2+ pump. Alanine and serine mutants of Tyr(801) located in the fifth transmembrane segment of the gastric proton pump alpha-subunit retained the Rb-86 transport and K+-dependent ATPase (K+-ATPase) activities. These mutants showed 60 - 80-times lower sensitivity to SCH 28080 than the wild type in the 86Rb transport activity. The K+-ATPase activities of these mutants were not completely inhibited by SCH 28080. The sensitivity to SCH 28080 was dependent on the bulkiness of the side chain at this position. Therefore, the side chain of Tyr(801) is important for the interaction with this inhibitor. In the three-dimensional structure of the E-2 form (conformation with high affinity for K+) of the gastric proton pump, Tyr(801) faces a cavity surrounded by the first, fourth, fifth, sixth, and eighth transmembrane segments and fifth/sixth, seventh/ eighth, and ninth/tenth loops. SCH 28080 can dock in this cavity. However, SCH 28080 cannot dock in the same location in the E-1 form ( conformation with high affinity for proton) of the gastric proton pump due to the drastic rearrangement of the transmembrane helices between the E-1 and E-2 forms. These results support the idea that this cavity is the binding pocket of SCH 28080.