KLIFS: A Knowledge-Based Structural Database To Navigate Kinase–Ligand Interaction Space

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• 作者：Oscar P. J. van Linden ; Albert J. Kooistra ; Rob Leurs ; Iwan J. P. de Esch ; Chris de Graaf
• 刊名：Journal of Medicinal Chemistry
• 出版年：2014
• 出版时间：January 23, 2014
• 年：2014
• 卷：57
• 期：2
• 页码：249-277
• 全文大小：2792K
• ISSN：1520-4804

文摘

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鈥搇igand interactions in all regions of the catalytic cleft of all 1252 human kinase鈥搇igand cocrystal structures present in the Protein Data Bank (PDB). The kinase鈥搇igand 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鈥搇igand 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.