Classification of common functional loops of kinase super-families

Proteins. 2004 Aug 15;56(3):539-55. doi: 10.1002/prot.20136.


A structural classification of loops has been obtained from a set of 141 protein structures classified as kinases. A total of 1813 loops was classified into 133 subclasses (9 betabeta(links), 15 betabeta(hairpins), 31 alpha-alpha, 46 alpha-beta and 32 beta-alpha). Functional information and specific features relating subclasses and function were included in the classification. Functional loops such as the P-loop (shared by different folds) or the Gly-rich-loop, among others, were classified into structural motifs. As a result, a common mechanism of catalysis and substrate binding was proved for most kinases. Additionally, the multiple-alignment of loop sequences made within each subclass was shown to be useful for comparative modeling of kinase loops. The classification is summarized in a kinase loop database located at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Catalytic Domain
  • Databases, Protein
  • Models, Chemical
  • Phosphotransferases / chemistry*
  • Phosphotransferases / classification*
  • Protein Kinases / chemistry
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Structural Homology, Protein
  • Structure-Activity Relationship


  • Phosphotransferases
  • Protein Kinases