Proton pump inhibitors (PPIs) have become top-selling drugs worldwide. They are prodrugs activated by protonation in highly acidic environments. They inhibit stomach acid secretion by covalently modifying the gastric H+/K+-ATPase. However, little is known about alternative activation mechanisms and target proteins in non-acidic environments. Employing a chemoproteomic approach in living cells, we find rabeprazole to form covalent conjugates with numerous zinc-binding proteins. We show that one of the main target proteins, density-regulated protein (DENR), is conjugated to rabeprazole through a cysteine residue forming part of the zinc-binding site. We propose that zinc acts as a Lewis acid, obviating the need for low pH, to promote the activation of PPIs in non-acidic environments. Our findings may aid the understanding of secondary drug effects and/or the repurposing of PPIs.