Structural study of the complex between human pepsin and a phosphorus-containing peptidic transition-state analog

The refined crystal structure of the complex between human pepsin and a syn thetic phosphonate inhibitor, Iva-Val-Val-Leu(P)-(O)Phe-Ala-Ala-OMe [Iva = isovaleryl, Leu(P) = the phosphinic acid analog of L-leucine, (O)Phe = L-3- phenyllactic acid, OMe = methyl ester], is presented. The structure was ref ined using diffraction data between 30 and 1.9 Angstrom resolution to a fin al R factor (Sigma \ \F-o\ - \F-c\ \/ Sigma \F-o\, where \F-o\ and \F-c\ ar e the observed and calculated structure-factor amplitudes, respectively) of 20.0%. The interactions of the inhibitor with the enzyme show the location s of the binding sites on the enzyme from S4 to S3'. Modeling of the inhibi tor binding to porcine pepsin shows very similar binding sires, except at S 4. Comparison of the complex structure with the structures of related inhib itors bound to penicillopepsin helps to rationalize the observed difference s in the binding constants. The convergence of reaction mechanisms and geom etries in different families of proteinases is also discussed.