The newly identified specific V-ATPase inhibitor, salicylihalamide A, is distinct from any previously identified V-ATPase inhibitors in that it inhibits only mammalian V-ATPases, but not those from yeast or other fungi (Boyd, M. R., Farina, C., Belfiore, P., Gagliardi, S., Kim, J. W., Hayakawa, Y., Beutler, J. A., McKee, T. C., Bowman, B. J., and Bowman, E. J. (2001) J. Pharmacol. Exp. Ther. 297, 114-120). In addition, salicylihalamide A does not compete with concanamycin or bafilomycin for binding to V-ATPase, indicating that it has a different binding site from those classic V-ATPase inhibitors (Huss, M., Ingenhorst, G., Konig, S., Gassel, M., Drose, S., Zeeck, A., Altendorf, K., and Wieczorek, H. (2002) J. Biol. Chem. 277, 40544-40548). By using purified bovine brain V-pump and its dissociated V(1) and V(0) sectors, we identified the recognition and binding site for salicylihalamide to be within the V(0) domain. Salicylihalamide does not inhibit the ATP hydrolysis activity of the dissociated V(1)-ATPase but inhibits the ATPase activity of the holoenzyme by inhibiting the V(0) domain. Salicylihalamide causes a dramatic redistribution of cytosolic V(1) from soluble to membrane-associated form, a change not observed in cells treated with either bafilomycin or NH(4)Cl. By synthesizing and characterizing a series of salicylihalamide derivatives, we investigated the structural determinants of salicylihalamide inhibition in terms of potency and reversibility, and used this information to suggest a possible binding mechanism.