Pharmacophore analysis involves identification of key chemical features, or pharmacophores, that are necessary for a ligand to interact with a particular protein target cavity . This can be done by analyzing the structure of known X-ray complexes and identifying common chemical features that are critical for binding . In the case of E3 ligases, there are several key structural features that are important for ligand binding, including the presence of a zinc-binding domain and a substrate-binding site . However, it is important to note that pharmacophore analysis is not always sufficient to accurately predict ligand binding affinity, as there might be other factors that influence bindings that are not captured by the pharmacophore model.