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We have previously characterised a number of E3 ligase pockets, including two ubiquitin-specific E3 ligases (UBE2I and UBE2S), one E3 ligase associated with the proteasome (CUL1), and two G-protein-coupled receptors (EPHX1 and EPHB6) [24]. These pockets are all located on the surface of the E3 enzymes and can engage in interactions with ligands through their charged or hydrophobic surfaces, but the extent of their affinity for a ligand varies between them. The affinity is inversely proportional to the size of the pocket, which is determined by the first two amino acid residues in the cavity (a larger pocket size requires a lower number of first two residues in the pocket), while the topology of the ligand might also affect the pocket size. The affinity of a ligand for a pocket is related to the number of non-bonded interactions, also known as electrostatic and van der Waals (vdW) interactions and vdW interactions are mainly mediated by the size and shape of the ligand. In the case of PROTACs, we have already predicted a new pocket [24], which is located in the catalytic domain of E3 ligase CUL5 on the surface of the enzyme and is characterised by a large size and hydrophobic cavity. However, the lack of ligands in the crystallographic structures has not allowed the verification of the ligand-binding potential of this pocket and, after that, its application in the design of PROTACs. Moreover, the large size of the pocket could affect the design of ligand scaffolds by blocking the interactions with the ligand. To overcome this issue, we have selected seven well-known ligands from the PDB database (Table 1), which are known to interact with the CUL5 pocket, and used them to conduct a virtual screening of the ELIOT pocketome. We have then analysed the MIFs of these seven ligands using our ELIOT platform, which has allowed us to identify the residues characterising the pocket.
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