| Index | Ligand Name | Structure | PDB code | ligand desolvation |
| 1 | 1ks | Structure of the human smoothened 7TM receptor in complex with an antitumor agent | 4jkv | 98.3 |
| 2 | snt | Structure of the human smoothened receptor in complex with SANT-1. | 4n4w | 98 |
| 3 | 836 | 3.0A SYN structure of the multi-domain human smoothened receptor in complex with TC114 | 5v57 | 97.59 |
| 4 | 836 | 2.9A XFEL structure of the multi-domain human smoothened receptor (with E194M mutation) in complex with TC114 | 5v56 | 97.22 |
| 5 | clr | Crystal structure of active Smoothened bound to SAG21k, cholesterol, and NbSmo8 | 6o3c | 97.14 |
| 6 | sg8 | Structure of the human smoothened receptor in complex with SAG1.5 | 4qin | 95.24 |
| 7 | lkd | Crystal structure of active Smoothened bound to SAG21k, cholesterol, and NbSmo8 | 6o3c | 95.03 |