Organotin-flavone complexes of 3-hydroxyflavone 3,5,7-trihydroxyflavone (galangin) and 2',3,4',5,7-pentahydroxyflavone (morin) are potent inhibitors of the vacuolar H(+)-translocating ATPase from bovine adrenal chromaffin granules, with K, values around 0.3 microM. The fluorescence of the 3-hydroxyflavone complex is enhanced on binding to the purified, reconstituted V-ATPase, and tributyltin reduces this fluorescence enhancement, though not strictly competitively. Radioiodinated derivatives of galangin and morin were synthesized and their organotin complexes were crosslinked to the ATPase by ultraviolet irradiation. Subunit A (72 kDa) of the V-ATPase was labelled, and tributyltin strongly inhibited this labelling. Subunits M115 and M39 were labelled less strongly and tributyltin did not affect this labelling. We conclude that there is a specific interaction between organotin compounds and V-ATPase subunit A, in the catalytic sector of the enzyme. This approach did not detect the recently-reported interaction between dibutyltin-3-hydroxyflavone bromide and the 16 kDa 'proteolipid' subunit of the V-ATPase.