| Index | Ligand Name | Structure | PDB code | ligand desolvation |
| 1 | 53z | Human Cyclophilin D Complexed with an Inhibitor | 4j58 | 83.36 |
| 2 | 728 | Human Cyclophilin D Complexed with an Inhibitor | 4j5d | 76.68 |
| 3 | 7b7 | Human Cyclophilin D Complexed with an Inhibitor | 4j5e | 75.96 |
| 4 | c4y | Human Cyclophilin D Complexed with Inhibitor | 5ccs | 75.23 |
| 5 | 4zz | Human Cyclophilin D Complexed with Inhibitor | 5ccn | 74.89 |
| 6 | 67z | Human Cyclophilin D Complexed with an Inhibitor | 4j5a | 73.46 |
| 7 | 6b4 | Human Cyclophilin D Complexed with an Inhibitor | 4j5b | 73.11 |
| 8 | 4zp | Human Cyclophilin D Complexed with Inhibitor | 5cbv | 73.02 |
| 9 | 671 | Human Cyclophilin D Complexed with an Inhibitor | 4j59 | 72.42 |
| 10 | bs4 | Human cyclophilin D complexed with N-[(4-aminophenyl)sulfonyl]benzamide | 3rcf | 65.26 |