Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

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...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Transducer Mechanism: Enzyme-Linked Receptors01:27

Transducer Mechanism: Enzyme-Linked Receptors

Enzyme-linked receptors are cell-surface receptors acting as an enzyme or associating with an enzyme intracellularly. They make excellent drug targets. Drugs can bind to the extracellular ligand-binding domain or directly affect their enzymatic domain and alter their activity.
Major types that are helpful drug targets include:
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

B-cell precursor acute lymphoblastic leukaemia with <i>IGH::CEBP</i> rearrangement: what have we learnt over the years?

Haematologica·2026
Same author

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.

Nature methods·2026
Same author

Comprehensive analysis of SARS-CoV-2 Spike evolution: epitope classification and immune escape prediction.

Virus evolution·2025
Same author

Chromothripsis-associated chromosome 21 amplification orchestrates transformation to blast-phase MPN through targetable overexpression of DYRK1A.

Nature genetics·2025
Same author

Measuring catalytic mechanism similarity - a new approach to study enzyme function and evolution.

The FEBS journal·2025
Same author

A structural perspective on enzymes and their catalytic mechanisms.

Current opinion in structural biology·2025

Related Experiment Video

Updated: Jun 19, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Domain-ligand mapping for enzymes.

Matthew Bashton1, Janet M Thornton

  • 1EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom. bashton@ebi.ac.uk

Journal of Molecular Recognition : JMR
|October 8, 2009
PubMed
Summary
This summary is machine-generated.

This paper maps small molecule ligands to protein domains, highlighting nature's most common ligand-protein interactions. It reviews available data resources and discusses potential applications of this knowledge.

More Related Videos

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Related Experiment Videos

Last Updated: Jun 19, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Understanding protein-ligand interactions is crucial in molecular biology.
  • Existing data resources offer valuable insights into these interactions.

Purpose of the Study:

  • To provide an overview of the current knowledge on small molecule ligand-protein domain mapping.
  • To discuss available web-based data resources and introduce the PROCOGNATE database.
  • To identify frequently utilized ligands in large protein superfamilies and explore potential data applications.

Main Methods:

  • Literature review of protein-ligand interaction data.
  • Database curation and analysis (PROCOGNATE).
  • Analysis of ligand binding patterns in protein superfamilies.

Main Results:

  • An overview of current understanding of protein-ligand mapping.
  • Identification of key data resources and the PROCOGNATE database.
  • Insights into common ligands used by nature across large protein families.

Conclusions:

  • The mapping of small molecules to protein domains is an evolving field.
  • Data resources like PROCOGNATE are essential for research.
  • Understanding ligand utilization has potential applications in drug discovery and protein engineering.