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KLIFS: a structural kinase-ligand interaction database.

Authors :: Kooistra AJ
Kanev GK
van Linden OP
Leurs R
de Esch IJ
de Graaf C
Source :: Nucleic acids research [Nucleic Acids Res] 2016 Jan 04; Vol. 44 (D1), pp. D365-71. Date of Electronic Publication: 2015 Oct 22.
Publication Year :: 2016
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.<br /> (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)