SMYD3 (SET- and MYND-domain containing protein 3) is an epigenetic enzyme with lysine methyl transferase activity and multiple protein binding partners. It is implicated in cancer development and active site inhibitors with antitumor activity have been developed. We have previously discovered that diperodon is an allosteric SMYD3 ligand and are interested in developing ligands that can interfere with non-catalytic functions of SMYD3, while avoiding conceivable draw-backs of targeting a conserved site in an enzyme with several close family members. Herein, the features of the diperodon site were explored via computational modelling and served as a basis for identifying analogues in commercial compound space, thus avoiding the need for in-house compound synthesis. Time-resolved grating coupled interferometry (GCI) biosensor analysis confirmed that two out of 21 acquired analogues interacted with SMYD3, with similar affinities as diperodon (K