Figure 7.

Surface area of ligand-enzyme interactions. Interactions are shown between A. 2c ligand and HDAC 4 Homo sapiens. B. 2a ligand and HDAC 5 Homo sapiens. C. 2c ligand and HDAC 6 Homo sapiens. D. 2c ligand and HDAC 7 Homo sapiens. E. 1c ligand and HDAC 9 Homo sapiens. F. 1c ligand and HDAC 10 Homo sapiens. These show that the cavity of enzyme is deep enough for ligand binding. The depth makes it necessary to utilize certain ligands with long aliphatic ring, in order for it to enter the cavity, and interact with Zn²⁺ ion. Hydrophobic cap group is necessary as well, in order to guarantee the interaction between ligand’s cap groups with enzyme’s surface area.