| Class | HDAC | Localization | Representative PDB code | Numbers of amino acids |
|---|---|---|---|---|
| I | 1 | Nuclear | 4BKX | 483 |
| 2 | Nuclear | 3MAX | 488 | |
| 3 | Nuclear/cytoplasmic | 4A69 | 428 | |
| 8 | Nuclear | 5VI6 | 377 | |
| IIA | 4 | Nuclear/cytoplasmic | 5ZOO | 1,084 |
| 5 | Nuclear/cytoplasmic | - | 1,122 | |
| 7 | Nuclear/cytoplasmic | 3C0Y | 912 | |
| 9 | Nuclear/cytoplasmic | 1TQE | 1,069 | |
| IIB | 6 | Cytoplasmic | 3PHD | 1,215 |
| 10 | Cytoplasmic | 6WDY | 669 | |
| IV | 11 | Nuclear | - | 347 |
-: not applicable; PDB: Protein Data Bank