Specific irreversible inhibition of the SIV protease by FMOC-protected piperidine epoxide 1 involves alkylation of the protein. Tryptic digestion of the alkylated protein and mass spectrometric analysis of the peptides identify an active site aspartic acid (Asp-25) as the single residue that is alkylated. Computer modeling of 1 bound in the crystal structure of the SIV protease using DOCK 3.5 indicates that 1 has appropriate access to the active site. It is able to align in an orientation that allows a proton to be transferred to the epoxide from one of the catalytic aspartic acid groups in conjunction with nucleophilic attack on the epoxide of the carboxylate moiety of the second catalytic aspartic acid residue. Hydrophobic interactions are not optimal for this process due, in part, to the rigidity of the inhibitor ring system and the planar conformation of the amide. The combination of modeling with protein alkylation can provide insights into structural modifications of the inhibitor that may lead to improved inhibitory activity.