The binding mode of CA074 [N-(L-3-trans-propylcarbamoyl-oxirane-2-carbonyl)-L-isoleucyl-L-proline] , a specific irreversible inhibitor, to bovine spleen cathepsin B was elucidated by X-ray crystal structure analysis of the complex at 2.2 Angstrom resolution (conventional R=0.185), Inconsistently with our model used for the development of CA074, the L-isoleucyl-L-proline and propylcarbamoyl moieties are located at the S' and S subsites respectively, This unexpected binding is primarily due to (i) similar extended chain conformations (due to the same S configurations) at the oxirane C2 and C3 atoms of CA074 and (ii) the just fit formation of double hydrogen bonds between the carboxyl oxygens of L-proline and the imidazole nitrogens of His-110 and His-ill residues (these residues are missing in papain, the tertiary structure of which was used for the design of CA074), The oxirane C3 atom possessing the P' substituent is covalently bound to the Cys-29 S gamma atom (C3-S gamma=1.79 Angstrom) and the S configuration is maintained. The present result will provide useful information for characterizing the substrate-specificity of cathepsin B.