Propargylic and activated allylic amines are known to inactivate the quinone-dependent plasma amine oxidases, possibly through active-site modification by the alpha,beta-unsaturated aldehyde turnover products. Although homopropargylamine (1-amino-3-butyne, 1) is a nonobvious candidate as a mechanism-based inhibitor, 1 was found to be an unusually potent time- and concentration-dependent irreversible inactivator of bovine plasma amine oxidase (BPAO), exhibiting a 30 min IC(50) of 2.9 microM at 30 degrees C ([BPAO] = 1.2 microM). Preserved cofactor redox activity of the denatured inactivated enzyme indicates that inactivation by 1 involves either a cofactor modification that reverses upon enzyme denaturation or a modification of an active-site residue. Because inactivation by 1 may involve enzyme alkylation by the reactive 2,3-butadienal (3) tautomer of the 3-butynal turnover product of 1, aldehyde 3 was prepared and was found to inactivate BPAO, but only at high concentration. In addition, whereas inhibition by 3 was blunted by the presence of mercaptoethanol, no such protection was observed against 1. The amine whose turnover should lead directly to 3 was prepared (1-amino-2,3-butadiene, 4) and was found to be an even more potent inactivator of BPAO than 1, exhibiting a 5 min IC(50) of 1.25 microM. Rat liver mitochondrial monoamine oxidase was also inactivated by 4, as expected, but only very weakly by 1. Potential mechanisms explaining the selective inhibition of BPAO by 1 are discussed.