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 ␣-subunit that was constructed by homology modeling based on the structure of sarcoplasmic reticulum Ca 2؉ pump. Alanine and serine mutants of Tyr 801 located in the fifth transmembrane segment of the gastric proton pump ␣-subunit retained the 86 Rb 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 86 Rb 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.The gastric H ϩ ,K ϩ -ATPase is a proton pump that is responsible for gastric acid secretion (1). This pump consists of two kinds of subunits, the ␣-and -subunits. The ␣-subunit is the catalytic subunit containing 10 transmembrane segments. The ATP binding site (2, 3) and the cation binding sites are located on this subunit (4 -10). The -subunit is the non-catalytic glycoprotein containing a single transmembrane segment and is involved in stabilization as well as targeting of the ␣-subunit to the plasma membrane (11). This pump belongs to the family of type II P-type ATPases, which include sarcoplasmic reticulum (SR) 1 Ca 2ϩ -ATPase (Ca 2ϩ pump) and Na ϩ ,K ϩ -ATPase (Na ϩ pump) (12).At present, inhibitors specific for the gastric proton pump are classified into two groups. Irreversible inhibitors such as omeprazole, rabeprazole, and lansoprazole, termed the proton pump inhibitors, are the first group. They are activated in acidic lumens, modify the cysteine residues located on the luminal side of the proton pump, and inhibit its pump activity. They are clinically used for controlling hyperacidity. The second classified group of specific proton pump inhibitors are the reversible inhibitors such as SCH 28080 (13) and 3-amino-5-methyl-2-(2-methyl-3-thienyl)imidazo[1,2-a]thieno[3,2-c]pyridine (SPI-447) (Fig. 1) (14), which are described as acid pump antagonists (APAs). They bind to the E 2 or E 2...