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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...
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...
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...
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...
Factors Affecting Protein-Drug Binding: Protein-Related Factors01:20

Factors Affecting Protein-Drug Binding: Protein-Related Factors

Drug binding to proteins is a key aspect of pharmacokinetics and can influence a drug's distribution, absorption, and elimination in the body. Several factors, including the drug's physiochemical properties, protein concentration, disease states, and the number of binding sites on the protein, influence this process.
The physicochemical properties of a drug play a significant role in its ability to bind to proteins. Lipophilic drugs, which dissolve in fats, oils, and lipids, can be bound by...

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Related Experiment Video

Updated: Jul 16, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Shape variation in protein binding pockets and their ligands.

Abdullah Kahraman1, Richard J Morris, Roman A Laskowski

  • 1European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK. abdullah@ebi.ac.uk

Journal of Molecular Biology
|March 6, 2007
PubMed
Summary

Protein binding pockets are not always the exact shape of their ligands. Pocket shape significantly contributes to molecular recognition, but pockets are often much larger than the bound ligand.

Related Experiment Videos

Last Updated: Jul 16, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Biophysics

Background:

  • A prevalent assumption in molecular biology is that protein binding pockets geometrically match their small molecule ligands.
  • The precise extent to which pocket shape dictates ligand binding remains an open question.

Purpose of the Study:

  • To quantitatively assess the relationship between protein binding pocket shape and ligand shape using a novel shape matching technique.
  • To determine the contribution of shape complementarity to molecular recognition.

Main Methods:

  • Utilized a recently developed shape matching algorithm to compare 3D shapes of protein binding pockets and their corresponding ligands.
  • Analyzed the conformational variability of ligands within binding pockets.

Main Results:

  • Observed significant shape variation among pockets binding the same ligand, exceeding ligand conformational flexibility.
  • Demonstrated that shape and size alone account for a substantial portion of a binding pocket's ligand recognition capability.
  • Identified a consistent 'buffer zone' of unoccupied space, indicating pockets are, on average, three times larger than their bound ligands.

Conclusions:

  • Geometrical complementarity alone is insufficient to fully explain molecular recognition.
  • Binding pocket shape is a critical determinant of ligand recognition, despite observed pocket-ligand size discrepancies.
  • The presence of a buffer zone suggests a more complex binding mechanism than simple steric fit.