Kinase-Ligand Interaction Fingerprints and Structures database (KLIFS), developed at the Division of Medicinal Chemistry - VU University Amsterdam, is a database that revolves around the protein structure of catalytic kinase domains and the way kinase inhibitors can interact with them. Based on the underlying systematic and consistent protocol all (currently human and mouse) kinase structures and the binding mode of kinase ligands can be directly compared to each other. Moreover, because of the classification of an all-encompassing binding site of 85 residues it is possible to compare the interaction patterns of kinase-inhibitors to each other to, for example, identify crucial interactions determining kinase-inhibitor selectivity.

Follow the tutorial, read our Nucleic Acids Research publication and ACS Journal of Medicinal Chemistry publication, or see the frequently asked questions (FAQ) for more information about the possibilities of KLIFS.

Animation of the stuctural kinome coverage through time here.

Latest news:

Release version 2.1


  • KNIME nodes for KLIFS developed within the 3D-e-Chem project. Use KNIME to delve into KLIFS and extract all data and structures from within your own workflows! Just add our 3D-e-Chem repository ( to KNIME, install the KLIFS nodes, and you are good to go (for more information see the GitHub repository).
  • Web services including Swagger API definition (here)
  • Kinome-through-time animation (here)
  • Links to IUPHAR - Guide to pharmacology
  • Predefined "lead-like properties" for the ligand properties search
  • Included MGI nomenclature for the mouse kinases
  • 3D viewer labels now shows KLIFS numbering
  • Detailed interactions overview now includes original X-ray numbering


  • Updated kinase classification and nomenclature
  • Improved 2D depiction of ligands, however, we are still working on further improvement
  • Updated the HGNC nomenclature and UniProt numbering
  • Updated ChEMBL integration to version 21
  • Included (p)Kd values in the bioactivity data overview


  • MOE database downloads did not always include all selected entries when NMR structures were encountered
  • CSV downloads could erroneously mark all entries as "human"
  • Issue for the 3D viewer on iOS devices: some structures were not visible
  • Issue for the 3D viewer when the N-term of a structure was in a helix
Species: 2
Groups: 8
Families: 89
Kinases: 256
PDB entries: 3386
Monomers: 7018
Unique ligands: 2113

Latest additions:
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