| Index | Ligand Name | Structure | PDB code | ligand desolvation |
| 1 | xu3 | CATHEPSIN L WITH A NITRILE INHIBITOR | 2xu3 | 70.68 |
| 2 | djt | CATHEPSIN L WITH A NITRILE INHIBITOR | 2xu4 | 68.79 |
| 3 | yj8 | CATHEPSIN L WITH A NITRILE INHIBITOR | 2yj8 | 68.64 |
| 4 | yj2 | CATHEPSIN L WITH A NITRILE INHIBITOR | 2yj2 | 68.48 |
| 5 | 424 | CATHEPSIN L WITH A NITRILE INHIBITOR | 2xu1 | 68.19 |
| 6 | 424 | CATHEPSIN L WITH A NITRILE INHIBITOR | 2yjc | 68.01 |
| 7 | 7kh | CATHEPSIN L IN COMPLEX WITH 4-[cyclopentyl(imidazo[1,2-a]pyridin-2-ylmethyl)amino]-6-morpholino-1,3,5-triazine-2-carbonitrile | 5maj | 67.16 |
| 8 | xu5 | CATHEPSIN L WITH A NITRILE INHIBITOR | 2xu5 | 65.72 |
| 9 | 5t9 | CATHEPSIN L IN COMPLEX WITH (2S,4R)-4-(2-Chloro-4-methoxy-benzenesulfonyl)-1-[3-(5-chloro-pyridin-2-yl)-azetidine-3-carbonyl]-pyrrolidine-2-carboxylic acid (1-cyano-cyclopropyl)-amide | 5f02 | 65.07 |
| 10 | c7t | CATHEPSIN L IN COMPLEX WITH (3S,14E)-8-(azetidin-3-yl)-19-chloro-N-(1-cyanocyclopropyl)-5-oxo-12,17-dioxa-4-azatricyclo[16.2.2.06,11]docosa-1(21),6,8,10,14,18(22),19-heptaene-3-carboxamide | 6f06 | 65.01 |
| 11 | v65 | TRIAZINE CATHEPSIN INHIBITOR COMPLEX | 4axm | 64.22 |
| 12 | 7kn | CATHEPSIN L IN COMPLEX WITH (2S,4R)-4-(2-Chloro-4-methoxy-benzenesulfonyl)-1-[3-(5-chloro-pyridin-2-yl)-azetidine-3-carbonyl]-pyrrolidine-2-car boxylic acid (1-cyano-cyclopropyl)-amide | 5mae | 59.88 |