What is a binding site?

A binding site (or binding pocket) is the part of a protein’s surface where another molecule — a substrate, a natural partner or a drug — attaches. Its shape, size and the chemistry of the amino acids lining it decide which molecules can bind.

Types of binding site

• Orthosteric sites are where the natural substrate or ligand binds, such as an enzyme’s active site. Drugs here compete directly with the natural binder.
• Allosteric sites are elsewhere on the protein. Binding there changes the protein’s shape or dynamics and indirectly alters its activity, which can give better selectivity between related proteins.
• Cryptic sites are pockets that are not visible in the unbound structure and only open when the protein moves or a ligand binds.
• Protein–protein interfaces are large, shallow surfaces where two proteins meet. They are hard to block with small molecules and are a key opportunity for macrocycles.

Druggability

A pocket is considered druggable when a drug-like molecule can bind it with high affinity. Deep, enclosed, mostly hydrophobic pockets with a few well-placed polar groups score best. Shallow, highly polar or very exposed sites are harder, though not impossible, to drug.

Finding and defining the site

1. From experiment: co-crystal or cryo-EM structures with a bound ligand show the site directly. Mutagenesis data also points to important residues.
2. From prediction: pocket-detection programs analyse the protein surface for cavities. AI structure models can also predict ligand-bound complexes; see protein structure prediction.
3. For docking: the site is usually described as a box centred on the pocket, with a few ångströms of margin around a known ligand. If the site is unknown, blind methods such as DiffDock can scan the whole protein.