| Index | Ligand Name | Structure | PDB code | ligand desolvation |
| 1 | 3xt | Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors. | 4x6h | 89.14 |
| 2 | i37 | Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors. | 4x6h | 85.24 |
| 3 | 2ca | CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT AZEPANONE INHIBITOR | 1nlj | 75.25 |
| 4 | 3y2 | Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors. | 4x6j | 73.9 |
| 5 | 3y1 | Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors. | 4x6i | 72.41 |
| 6 | noq | A mutant rabbit cathepsin K with a nitrile inhibitor | 2f7d | 72.36 |
| 7 | 0lc | Cathepsin K inhibitor | 4dmy | 72.18 |
| 8 | 1xf | Human cathepsin K mutant C25S in complex with the allosteric effector NSC13345 | 5j94 | 71.05 |
| 9 | i10 | CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT PEPTIDOMIMETIC INHIBITOR | 1bgo | 69.88 |
| 10 | 3fc | Cathepsin K complexed with a constrained ketoamide inhibitor | 1yt7 | 67.2 |
| 11 | cke | Crystal structure of a pyrrolopyrimidine inhibitor in complex with human Cathepsin K | 2r6n | 66.73 |
| 12 | orh | Structure of CatK covalently bound to a dioxo-triazine inhibitor | 3kwb | 66.67 |
| 13 | o96 | Cathepsin K in complex with a covalent inhibitor with a ketoamide warhead | 3ovz | 66.64 |
| 14 | pos | CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT PROPANONE INHIBITOR | 1au2 | 66.36 |
| 15 | 7as | Crystal structure of Cathepsin K with a covalently-linked inhibitor at 1.4 Angstrom resolution. | 5tdi | 65 |
| 16 | kwz | Cathepsin K in complex with a non-selective 2-cyano-pyrimidine inhibitor | 3kwz | 64.57 |
| 17 | ihi | Crystal Structure of the Cysteine Protease Human Cathepsin K in Complex with the Covalent Inhibitor NVP-ABI491 | 1u9w | 62.28 |
| 18 | o75 | Cathepsin K covalently bound to a 2-cyano pyrimidine inhibitor with a benzyl P3 group. | 3o1g | 62.22 |
| 19 | 4pr | Cathepsin K complexed with a pyrrolidine ketoamide-based inhibitor | 2bdl | 59.19 |
| 20 | ihe | Crystal Structure of the Cysteine Protease Human Cathepsin K in Complex with the Covalent Inhibitor NVP-ABE854 | 1u9v | 55.66 |
| 21 | ihj | Crystal Structure of the Cysteine Protease Human Cathepsin K in Complex with the Covalent Inhibitor NVP-ABJ688 | 1u9x | 54.05 |
| 22 | kx1 | Cathepsin K in complex with a selective 2-cyano-pyrimidine inhibitor | 3kx1 | 52.11 |