| Index | Ligand Name | Structure | PDB code | Compound Potency nM |
| 1 | y11 | Cathepsin S complexed with Compound 15 | 2r9m | 1.5 |
| 2 | 2fz | Crystal Structure of Human Cathepsin S Bound to a Non-covalent Inhibitor. | 4p6g | 7.7 |
| 3 | ef3 | 6-Phenyl-1H-imidazo[4,5-c]pyridine-4-carbonitrile as cathepsin S inhibitors | 3n4c | 9.5 |
| 4 | gnf | Cathepsin S in complex with non-covalent 2-(Benzoxazol-2-ylamino)-acetamide | 2f1g | 29 |
| 5 | o64 | Cathepsin S in complex with a covalent inhibitor with an aldehyde warhead | 3ovx | 31 |
| 6 | 93n | 4-(3-Trifluoromethylphenyl)-pyrimidine-2-carbonitrile as cathepsin S inhibitors: N3, not N1 is critically important | 3n3g | 58 |
| 7 | bc7 | Crystal structure of human Cathepsin-S with bound ligand | 5qc4 | 150 |
| 8 | 599 | Pyrazole-based Cathepsin S Inhibitors with Arylalkynes as P1 Binding Elements | 3iej | 220 |
| 9 | 2fc | Crystal Structure of Human Cathepsin S Bound to a Non-covalent Inhibitor | 4p6e | 1290 |