| Index | Ligand Name | Structure | PDB code | ligand desolvation |
| 1 | 2fc | Crystal Structure of Human Cathepsin S Bound to a Non-covalent Inhibitor | 4p6e | 85.06 |
| 2 | h7j | Crystal Structure of Cathepsin S in complex with a Nonpeptidic Inhibitor. | 2h7j | 78.69 |
| 3 | ef3 | 6-Phenyl-1H-imidazo[4,5-c]pyridine-4-carbonitrile as cathepsin S inhibitors | 3n4c | 77.48 |
| 4 | h7j | Crystal Structure of Cathepsin S in complex with a Nonpeptidic Inhibitor (Hexagonal spacegroup) | 2hxz | 76.44 |
| 5 | 935 | 4-(3-Trifluoromethylphenyl)-pyrimidine-2-carbonitrile as cathepsin S inhibitors: N3, not N1 is critically important | 3n3g | 76.34 |
| 6 | crj | Cathepsin S with nitrile inhibitor | 2fq9 | 75.36 |
| 7 | crv | Human Cathepsin S with CRA-27934, a Nitrile Inhibitor | 2fra | 75.22 |
| 8 | o64 | Cathepsin S in complex with a covalent inhibitor with an aldehyde warhead | 3ovx | 75.19 |
| 9 | mo9 | Human Cathepsin S with inhibitor CRA-16981 | 2g7y | 74.63 |
| 10 | y14 | Cathepsin S complexed with Compound 26 | 2r9n | 73.63 |
| 11 | c28 | Human Cathepsin S with Inhibitor CRA-29728 | 2ft2 | 73.2 |
| 12 | y11 | Cathepsin S complexed with Compound 15 | 2r9m | 72.78 |
| 13 | 93n | 4-(3-Trifluoromethylphenyl)-pyrimidine-2-carbonitrile as cathepsin S inhibitors: N3, not N1 is critically important | 3n3g | 71 |
| 14 | gnf | Cathepsin S in complex with non-covalent 2-(Benzoxazol-2-ylamino)-acetamide | 2f1g | 70.95 |
| 15 | 599 | Pyrazole-based Cathepsin S Inhibitors with Arylalkynes as P1 Binding Elements | 3iej | 61.4 |
| 16 | 2fz | Crystal Structure of Human Cathepsin S Bound to a Non-covalent Inhibitor. | 4p6g | 61.04 |
| 17 | b9y | Crystal structure of human Cathepsin-S with bound ligand | 5qc3 | 60.81 |
| 18 | c71 | Human Cathepsin S with Inhibitor CRA-26871 | 2frq | 60.45 |
| 19 | bjs | Crystal structure of human Cathepsin-S with bound ligand | 5qch | 58.37 |
| 20 | b9s | Crystal structure of human Cathepsin-S with bound ligand | 5qc1 | 57.05 |
| 21 | bc7 | Crystal structure of human Cathepsin-S with bound ligand | 5qc4 | 56.73 |
| 22 | b8j | Crystal structure of human Cathepsin-S with bound ligand | 5qbu | 55.07 |
| 23 | bg7 | Crystal structure of human Cathepsin-S with bound ligand | 5qc9 | 54.72 |
| 24 | bjy | Crystal structure of human Cathepsin-S with bound ligand | 5qcj | 54.11 |
| 25 | b8y | Crystal structure of human Cathepsin-S with bound ligand | 5qbz | 53.28 |