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PepX contains 505 unique protein-peptide interface clusters from 1431 PDBs, representing the diversity of structural information on protein-peptide complexes available in the Protein Data Bank. 47% of all protein-peptide complexes available from the PDB are clustered within only 10 classes, containing complexes with peptides bound to MHC, thrombins, α-ligand binding domains, SH3 domains, PDZ domains and other (see Figure on the right).

References

  • Vanhee, P., J. Reumers, et al. (2009). "PepX: A structural database of non-redundant protein-peptide complexes" NAR Database Issue 2009.pubmed.gif
  • Vanhee, P., F. Stricher, et al. (2009). "Protein-peptide interactions adopt the same structural motifs as monomeric protein folds." Structure, August 2009. pubmed.gif

Example protein-peptide complexes from PepX

18
ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OF SER190 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS
blood clotting, h2o displacement, Hydrolase, Selectivity at s1, ser190/ala190 protease, structure-based drug design, tpa, upa
15
COMPLEX OF THROMBIN WITH DESIGNED INHIBITOR 7165
blood coagulation, calcium-binding, glycoprotein, Hydrolase, plasma, serine protease
89
HUMAN THROMBIN-INHIBITOR COMPLEX
Complex (serine protease/inhibitor), Hydrolase
46
HUMAN THROMBIN HIRUGEN INHIBITOR COMPLEX.
acute phase, blood coagulation, calcium, disease mutation, gamma-carboxyglutamic acid, glycoprotein, Hydrolase, inhibitor, kringle, polymorphism, Protease, protease inhibitor, serine protease, serine protease inhibitor, sulfation, thrombin, zymogen
more
The binding interface of the protein-peptide complex is shown in grey, the peptide is shown in red. Note that only the interface of the protein-peptide complex is shown. Gaps between residues may occur.