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Positioning of compound 7 into the binding site of HDAC homologue, histone deacetylase-like protein (HDLP). The crystal structure of HDLP from Aquifex aeolicus complexed with the pan-HDAC inhibitor Trichostatin A (PDB code 1C3P; 1.8Å) was used for de novo design of KDACi using SPROUT. This configured the binding mode as “heel-leg-exit”, analogous to that for benzamide-headgroup KDACi.

Journal: Journal of Enzyme Inhibition and Medicinal Chemistry

Article Title: Development of novel benzamide class I selective lysine deacetylase inhibitors as potent anticancer agents

doi: 10.1080/14756366.2025.2520612

Figure Lengend Snippet: Positioning of compound 7 into the binding site of HDAC homologue, histone deacetylase-like protein (HDLP). The crystal structure of HDLP from Aquifex aeolicus complexed with the pan-HDAC inhibitor Trichostatin A (PDB code 1C3P; 1.8Å) was used for de novo design of KDACi using SPROUT. This configured the binding mode as “heel-leg-exit”, analogous to that for benzamide-headgroup KDACi.

Article Snippet: Total zinc-dependent KDAC (classes I, II and IV) activity was measured using the Fluor-de-Lys TM HDAC fluorometric activity assay kit (BioMol, Exeter, UK), as per manufacturers protocol.

Techniques: Binding Assay, Histone Deacetylase Assay