Binding Pocket

Understanding Protein Binding Pockets 

Welcome! This guide will introduce you to one of the most fundamental concepts in biochemistry and drug discovery: the protein binding pocket. We'll break it down step-by-step to make it easy to learn.

We need to understand that proteins are not just static chains of amino acids that are incorporated together. Proteins can fold into complex three-dimensional (3D) structures that allow them to interact with other molecules and perform essential biological functions — from catalyzing reactions to transporting molecules, transmitting signals, or regulating cellular activities, all of which are functions of proteins.

In drug design and discovery, one of the most important aspects of protein function is the region where molecules bind, or where small molecules interact with the protein; this is where terms like binding site and binding pocket come in. In most research articles, the binding site and the binding pocket are often used interchangeably, but they are not really the same thing. Understanding the difference is crucial, especially in the context of computer-aided drug design (CADD) and binding site prediction tools.

Binding Site vs. Binding Pocket: What's the Difference? 

A binding site is the part of a protein where a ligand (a small molecule, ion, peptide, or protein partner) binds. It is made up of all the amino acid residues and structural parts that help with recognition and binding. The ligand and the protein interact with each other through hydrogen bonds, ionic bonds, and hydrophobic interactions etc. These interactions are used to define the binding site.

A binding pocket is a three-dimensional space, groove, or hollow in the binding site where the ligand (or part of it) fits.

The binding site is like a specific set of "contacts," and the binding pocket is like a "socket" that holds them.

The idea of a physical pocket is most important for making small-molecule drugs that need to fit into proteins like a key fits into a lock. So, during this tutorial, we will mostly use the term "binding pocket," but keep in mind that it refers to the structural cavity that holds the functional binding site.

What is a binding pocket? 

A binding pocket is a three-dimensional region in a protein, which can be a concave area on or inside a protein where a ligand, ion, substrate, or another protein can specifically bind. 

A Lock and Key Analogy

In the first part of the molecular docking tutorial, we talked about the lock and key analogy.

Think of a protein as a machine that does a specific job in the body.

A protein's binding pocket is shaped and chemically designed to recognise and bind to a specific molecule called a ligand. When the ligand ("key") fits into the binding pocket ("lock"), it turns the protein "on" or "off," which has a specific effect on the body. The lock is a big biological machine that makes proteins. A ligand is the smaller molecule that attaches to the protein (the key). The binding pocket is the exact spot on the protein where the ligand fits (Figure 1).

What a binding pocket looks like

A binding pocket is not just an empty hole. Several key characteristics determine its ability to recognize a specific ligand:

Size and Shape (Steric Complementarity): The pocket volume and three-dimensional shape of a binding pocket are precisely tailored to its target ligand (small molecules). A bulky ligand cannot fit into a small pocket, and a small ligand will not bind effectively in an overly large one. This is an essential aspect: "the right key should be used for the right lock."

Physicochemical Properties: The amino acid residues present in the pocket give it unique chemical properties that must be complementary to the ligand.

Hydrophobicity: Pockets that contain non-polar amino acids create a water-repelling (hydrophobic) environment. They prefer to bind with non-polar parts of a ligand.

Polarity and Charge: Pockets containing charged (e.g., Aspartate, Lysine) or polar (e.g., Serine, Asparagine) residues can form powerful hydrogen bonds and ionic bonds (salt bridges) with complementary groups on the ligand.

Flexibility (Induced Fit): Proteins are not rigid, static structures. A binding pocket can be flexible, subtly changing its shape to accommodate a binding ligand. This dynamic adjustment, known as induced fit, often results in a tighter and more specific interaction.