KLIFS: a structural kinase-ligand interaction database

Nucleic Acids Res. 2016 Jan 4;44(D1):D365-71. doi: 10.1093/nar/gkv1082. Epub 2015 Oct 22.

Abstract

Protein kinases play a crucial role in cell signaling and are important drug targets in several therapeutic areas. The KLIFS database contains detailed structural kinase-ligand interaction information derived from all (>2900) structures of catalytic domains of human and mouse protein kinases deposited in the Protein Data Bank in order to provide insights into the structural determinants of kinase-ligand binding and selectivity. The kinase structures have been processed in a consistent manner by systematically analyzing the structural features and molecular interaction fingerprints (IFPs) of a predefined set of 85 binding site residues with bound ligands. KLIFS has been completely rebuilt and extended (>65% more structures) since its first release as a data set, including: novel automated annotation methods for (i) the assessment of ligand-targeted subpockets and the analysis of (ii) DFG and (iii) αC-helix conformations; improved and automated protocols for (iv) the generation of sequence/structure alignments, (v) the curation of ligand atom and bond typing for accurate IFP analysis and (vi) weekly database updates. KLIFS is now accessible via a website (http://klifs.vu-compmedchem.nl) that provides a comprehensive visual presentation of different types of chemical, biological and structural chemogenomics data, and allows the user to easily access, compare, search and download the data.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Agammaglobulinaemia Tyrosine Kinase
  • Animals
  • Catalytic Domain
  • Databases, Protein*
  • Humans
  • Internet
  • Ligands
  • Mice
  • Molecular Sequence Annotation
  • Protein Kinase Inhibitors / chemistry
  • Protein Kinases / chemistry*
  • Protein Kinases / metabolism
  • Protein-Tyrosine Kinases / antagonists & inhibitors

Substances

  • Ligands
  • Protein Kinase Inhibitors
  • Protein Kinases
  • Protein-Tyrosine Kinases
  • Agammaglobulinaemia Tyrosine Kinase