| Index | Ligand Name | Structure | PDB code | ligand desolvation |
| 1 | tfg | Structure of HDAC4 catalytic domain (a double cysteine-to-alanine mutant) bound to a trifluoromethylketone inhbitor | 2vqq | 95.03 |
| 2 | tfg | Structure of HDAC4 catalytic domain with a gain-of-function muation bound to a trifluoromethylketone inhbitor | 2vqo | 93.86 |
| 3 | otf | Potent, selective and CNS-penetrant tetrasubstituted cyclopropane class IIa histone deacetylase (HDAC) inhibitors | 5a2s | 78.77 |
| 4 | ebe | Development and characterization of a CNS-penetrant benzhydryl hydroxamic acid class IIa histone deacetylase inhibitor | 6fyz | 78.58 |
| 5 | kee | Design, synthesis, and biological evaluation of potent and selective Class IIa HDAC inhibitors as a potential therapy for Huntington's disease | 4cby | 76.3 |
| 6 | tfg | Structure of HDAC4 catalytic domain bound to a trifluoromethylketone inhbitor | 2vqj | 55.14 |
| 7 | ha3 | Structure of HDAC4 catalytic domain bound to a hydroxamic acid inhbitor | 2vqm | 50.05 |