KLIFS: a knowledge-based structural database to navigate kinase-ligand interaction space

O.P.J. van Linden, A.J. Kooistra, R. Leurs, I.J.P. de Esch, C. de Graaf

Research output: Contribution to JournalArticleAcademicpeer-review


Protein kinases regulate the majority of signal transduction pathways in cells and have become important targets for the development of designer drugs. We present a systematic analysis of kinase-ligand interactions in all regions of the catalytic cleft of all 1252 human kinase-ligand cocrystal structures present in the Protein Data Bank (PDB). The kinase-ligand interaction fingerprints and structure database (KLIFS) contains a consistent alignment of 85 kinase ligand binding site residues that enables the identification of family specific interaction features and classification of ligands according to their binding modes. We illustrate how systematic mining of kinase-ligand interaction space gives new insights into how conserved and selective kinase interaction hot spots can accommodate the large diversity of chemical scaffolds in kinase ligands. These analyses lead to an improved understanding of the structural requirements of kinase binding that will be useful in ligand discovery and design studies.

Original languageEnglish
Pages (from-to)249-277
Number of pages29
JournalJournal of Medicinal Chemistry
Issue number2
Publication statusPublished - 2013


  • Binding Sites
  • Data Mining
  • Databases, Protein
  • Drug Discovery
  • Humans
  • Hydrogen Bonding
  • Knowledge Bases
  • Ligands
  • Models, Molecular
  • Protein Binding
  • Protein Conformation
  • Protein Kinase Inhibitors
  • Protein Kinases
  • Journal Article
  • Research Support, Non-U.S. Gov't


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