As we know, ligands bind to receptors and activate them. But what is the relationship between the shape of a ligand and the shape of a receptor? You might think that all shapes would fit into any receptor or vice versa – but it turns out there is a definite pattern!
The binding site for most drugs on their target protein are either concave or convex in order to match up with the corresponding concave or convex pocket on the protein. The two examples below show how a drug that is designed to bind with the receptor can be matched by its shape.
The blue ligand in the first example has a concave binding site, and fits into the corresponding convex pocket on the protein like puzzle pieces. Similarly for yellow, which has a convex shape- it will fit nicely inside of an opposite-shaped concave binding site!
Conversely, if you look at these two molecules: green and red – they do not match up equally well because one molecule (green) has irregular edges while another (red) is mostly flat. Even though both have similar shapes, only one of them matches properly when placed against its specific receptor protein. Ligand-Re
