| Index | Ligand Name | Structure | PDB code | ligand desolvation |
| 1 | kln | Crystal structure of human P450 3A4 in complex with ketoconazole | 2v0m | 97.88 |
| 2 | mwv | Human CYP3A4 bound to a drug mibefradil | 6oo9 | 95.59 |
| 3 | 08y | Crystal structure of the cytochrome P4503A4-bromoergocryptine complex | 3ua1 | 93.47 |
| 4 | 08y | Crystal structure of the cysteine depleted CYP3A4 bound to bromoergocryptine | 5vcg | 92.97 |
| 5 | mws | Human CYP3A4 bound to a suicide substrate | 6oob | 92.1 |
| 6 | dj1 | Crystal structure of human CYP3A4 bound to an inhibitor | 6bdk | 89.98 |
| 7 | 08j | Crystal structure of the midazolam-bound human CYP3A4 | 5te8 | 89.89 |
| 8 | 6aw | Complex of CYP3A4 with a desoxyritonavir analog | 4k9v | 89.85 |
| 9 | d81 | Crystal structure of human CYP3A4 bound to an inhibitor | 6bd8 | 89.58 |
| 10 | tpf | Human CYP3A4 bound to an inhibitor fluconazole | 6ma7 | 89.16 |
| 11 | d7m | Crystal structure of human CYP3A4 bound to an inhibitor | 6bd5 | 88.46 |
| 12 | 2qh | Crystal structure of CYP3A4 in complex with an inhibitor | 4ny4 | 87.62 |
| 13 | myt | Human CYP3A4 bound to an inhibitor metyrapone | 6ma6 | 86.39 |
| 14 | 8aw | Complex of human CYP3A4 with a desoxyritonavir analog | 4k9x | 83 |
| 15 | d0r | Crystal Structure of the complex between human cytochrome P450 3A4 and desthiazolylmethyloxycarbonyl ritonavir | 3tjs | 80.23 |
| 16 | myt | Crystal structure of human cytochrome P450 3A4 | 1w0g | 76.83 |
| 17 | mwy | Human CYP3A4 bound to a drug substrate | 6ooa | 73.41 |
| 18 | str | Crystal structure of cytochrome P450 3A4 bound to progesterone | 5a1r | 48.49 |
| 19 | str | Crystal structure of cytochrome P450 3A4 bound to progesterone and citrate | 5a1p | 48.13 |
| 20 | str | Crystal structure of human cytochrome P450 3A4 | 1w0f | 47.31 |