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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
Receptor Tyrosine Kinases01:26

Receptor Tyrosine Kinases

Receptor tyrosine kinases or RTKs are membrane-bound receptors that phosphorylate specific tyrosine on protein substrates. RTKs regulate cellular growth, differentiation, survival, and migration. They contain an extracellular ligand binding domain, a transmembrane domain, and a cytosolic tail with intrinsic kinase activity. Several extracellular signaling molecules activate RTKs in one or more ways and relay the signal downstream. Ligands such as platelet-derived growth factor (PDGF) or...

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Updated: May 8, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
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A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

KLIFS: a knowledge-based structural database to navigate kinase-ligand interaction space.

Oscar P J van Linden1, Albert J Kooistra, Rob Leurs

  • 1Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

Journal of Medicinal Chemistry
|August 15, 2013
PubMed
Summary

This study systematically analyzes human kinase-ligand interactions using the KLIFS database. It reveals conserved interaction hotspots accommodating diverse chemical scaffolds, aiding drug discovery.

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Kinase Inhibitor Screening In Self-assembled Human Protein Microarrays
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Kinase Inhibitor Screening In Self-assembled Human Protein Microarrays

Published on: October 23, 2019

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Last Updated: May 8, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Kinase Inhibitor Screening In Self-assembled Human Protein Microarrays
13:22

Kinase Inhibitor Screening In Self-assembled Human Protein Microarrays

Published on: October 23, 2019

Area of Science:

  • Biochemistry
  • Structural Biology
  • Pharmacology

Background:

  • Protein kinases are crucial regulators of cellular signal transduction.
  • Kinases are key targets for developing novel therapeutic drugs.
  • Understanding kinase-ligand interactions is vital for drug design.

Purpose of the Study:

  • To systematically analyze kinase-ligand interactions across all regions of the catalytic cleft.
  • To classify ligands based on their binding modes within kinase structures.
  • To identify conserved and selective interaction features for drug design.

Main Methods:

  • Analysis of 1252 human kinase-ligand cocrystal structures from the Protein Data Bank (PDB).
  • Utilized the Kinase-Ligand Interaction Fingerprints and Structure (KLIFS) database.
  • Consistent alignment of 85 kinase ligand binding site residues.

Main Results:

  • Identified family-specific interaction features within kinase binding sites.
  • Classified diverse chemical scaffolds based on their binding modes.
  • Revealed conserved 'hot spots' in kinase binding sites accommodating varied ligands.

Conclusions:

  • Systematic analysis provides new insights into kinase-ligand interactions.
  • Understanding structural requirements enhances kinase inhibitor drug discovery and design.
  • KLIFS database facilitates exploration of kinase-ligand interaction space.