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

Acta Crystallogr D Biol Crystallogr. 2000 Mar;56(Pt 3):272-9. doi: 10.1107/s0907444999016376.


The refined crystal structure of the complex between human pepsin and a synthetic 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 refined using diffraction data between 30 and 1.96 A resolution to a final R factor ( summation operator| |F(o)| - |F(c)| | / summation operator|F(o)|, where |F(o)| and |F(c)| are the observed and calculated structure-factor amplitudes, respectively) of 20.0%. The interactions of the inhibitor with the enzyme show the locations of the binding sites on the enzyme from S4 to S3'. Modeling of the inhibitor binding to porcine pepsin shows very similar binding sites, except at S4. Comparison of the complex structure with the structures of related inhibitors bound to penicillopepsin helps to rationalize the observed differences in the binding constants. The convergence of reaction mechanisms and geometries in different families of proteinases is also discussed.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Aspartic Acid Endopeptidases / antagonists & inhibitors
  • Aspartic Acid Endopeptidases / chemistry
  • Aspartic Acid Endopeptidases / metabolism
  • Binding Sites
  • Chymotrypsin / antagonists & inhibitors
  • Chymotrypsin / chemistry
  • Crystallography, X-Ray
  • Humans
  • Hydrogen Bonding
  • Hydrolysis
  • Macromolecular Substances
  • Models, Molecular
  • Molecular Sequence Data
  • Oligopeptides / chemistry*
  • Oligopeptides / metabolism
  • Pepsin A / antagonists & inhibitors
  • Pepsin A / chemistry*
  • Pepsin A / metabolism
  • Protein Binding
  • Protein Conformation
  • Thermolysin / chemistry
  • Thermolysin / metabolism
  • Trypsin Inhibitor, Kazal Pancreatic / chemistry
  • Trypsin Inhibitor, Kazal Pancreatic / metabolism
  • Trypsin Inhibitor, Kazal Pancreatic / pharmacology


  • Macromolecular Substances
  • Oligopeptides
  • isovaleryl-valyl-valyl-leucinephosphinate-3-phenyllactic acid, alanyl-alanyl methyl ester
  • ovomucoid inhibitors
  • Trypsin Inhibitor, Kazal Pancreatic
  • Chymotrypsin
  • aspartic proteinase A
  • Aspartic Acid Endopeptidases
  • Pepsin A
  • Thermolysin

Associated data

  • PDB/1QRP