| Index | Ligand Name | Structure | PDB code | ligand desolvation |
| 1 | ha6 | Crystal structure of human KDM4D in complex with 2-1H-pyrazol-4-yloxy- 3H,4H-pyrido-3,4-d-pyrimidin-4-one | 5fpb | 94.89 |
| 2 | 5v0 | Crystal Structure of human JMJD2D complexed with KDOAM16 | 5f5a | 94.01 |
| 3 | 5v3 | Crystal Structure of human JMJD2D complexed with KDOPP7 | 5f5c | 90.39 |
| 4 | cqt | Crystal Structure of KDM4D with tetrazole ligand GF049 | 6f5s | 86.97 |
| 5 | yc8 | Crystal structure of human KDM4D in complex with 3-(4- phenylbutanamido)pyridine-4-carboxylic acid | 5fp4 | 86.39 |
| 6 | yc8 | Crystal structure of human KDM4D in complex with 3-4-methylthiophen-2- yl methylaminopyridine-4-carboxylic acid | 5fp7 | 86.39 |