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 2.2 - the Virtual Reality release


  • Virtual Reality: Google Cardboard viewer for mobile devices (visit KLIFS on your mobile phone). View the demo on YouTube
  • A mobile landing page for easy access to the Virtual Reality viewer
  • Weekly updates of PubMed identifiers
  • Weekly updates article DOIs for PDB entries
  • Weekly updated annotation of obsoleted and superseded PDB structures
  • A new release of the 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).


  • 2D ligand depictions are now generated with CACTVS
  • 2D depictions of allosteric ligands are now custom generated (replaces the depiction from the RCSB)


  • Small bug that caused an incorrect pocket overview for two structures
  • Several missing images of the 2D molecular structure of the ligand
  • Manually added two missing PDBs that were somehow not returned by the RCSB web services
  • Small bug in the RCSB web services that caused an error upon species selection
  • The interaction fingerprint was padded with too many zeroes in the MDB download option
  • Bug that could lead to the faulty annotation of ligands with a PDB-code starting with a Q
  • Issue when processing Ruthenium-containing ligands (again) that lead to the removal of the ligand


We would like to especially thank all KLIFS users that reported issues and/or requested new features. Your input is crucial to maintain a high quality database.

Species: 2
Groups: 8
Families: 89
Kinases: 258
PDB entries: 3446
Monomers: 7152
Unique ligands: 2167

Latest additions:
CSNK2A1CK2CMGCmethyl 3-[(3-{[(2-chlorobiphenyl-4-yl)methyl]amino}propyl)amino]-3-oxopropanoate
CSNK2A1CK2CMGCmethyl 3-[(3-{[(2-chlorobiphenyl-4-yl)methyl]amino}propyl)amino]-3-oxopropanoate
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