| Index | Ligand Name | Structure | PDB code | ligand desolvation |
| 1 | whh | Crystal structure of the catalytic domain of MMP-13 complexed with 4-(2-((6-fluoro-2-((3-methoxybenzyl)carbamoyl)-4-oxo-3,4-dihydroquinazolin-5-yl)oxy)ethyl)benzoic acid | 3wv1 | 92.27 |
| 2 | pb5 | Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor | 1xur | 91.85 |
| 3 | gg1 | MMP13 Catalytic Domain Complexed with 4-{[1-methyl-2,4-dioxo-6-(3-phenylprop-1-yn-1-yl)-1,4-dihydroquinazolin-3(2H)-yl]methyl}benzoic acid | 2ozr | 91.53 |
| 4 | 3ke | Crystal Structure of Human MMP-13 complexed with a phenyl-2H-tetrazole compound | 3kec | 90.86 |
| 5 | pb4 | Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor | 1xud | 90.19 |
| 6 | pb3 | Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor | 1xuc | 90 |
| 7 | 3ej | Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound | 3kej | 89.83 |
| 8 | 3ek | Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound | 3kek | 89.49 |
| 9 | wgg | Crystal structure of the catalytic domain of MMP-13 complexed with N-(3-methoxybenzyl)-4-oxo-3,4-dihydroquinazoline-2-carboxamide | 3wv2 | 89.26 |
| 10 | 4uf | X-RAY Co-structure of MMP-13 with 4-[({5-[2-(ethoxycarbonyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl}formamido)methyl]benzoate | 5bpa | 87.87 |
| 11 | wll | Crystal structure of the catalytic domain of MMP-13 complexed with N-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide | 3wv3 | 86.71 |
| 12 | 8oj | Matrix metalloproteinase-13 complexed with selective inhibitor compound (S)-17a | 5uwl | 85.67 |
| 13 | 8om | Matrix metalloproteinase-13 complexed with selective inhibitor compound (S)-10a | 5uwk | 83.14 |
| 14 | wnn | Crystal structure of the catalytic domain of MMP-13 complexed with 4-oxo-N-(3-(2-(1H-1,2,4-triazol-3-ylsulfanyl)ethoxy)benzyl)-3,4-dihydroquinazoline-2-carboxamide | 5b5p | 83.05 |
| 15 | cbp | STRUCTURE OF RECOMBINANT MOUSE COLLAGENASE-3 (MMP-13) | 1cxv | 80.77 |
| 16 | az4 | Mmp13 in complex with a reverse hydroxamate Zn-binder | 4jp4 | 79.78 |
| 17 | rs1 | COLLAGENASE-3 (MMP-13) COMPLEXED TO A SULPHONE-BASED HYDROXAMIC ACID | 830c | 79.19 |
| 18 | 24f | Crystal Structure of MMP-13 Complexed with Inhibitor 24f | 3elm | 78.87 |
| 19 | cbp | CRYSTAL STRUCTURE OF COLLAGENASE-3 (MMP-13) COMPLEXED TO A DIPHENYL-ETHER SULPHONE BASED HYDROXAMIC ACID | 456c | 77.95 |
| 20 | az6 | Mmp13 in complex with a piperazine hydantoin ligand | 4jpa | 77.5 |
| 21 | 033 | Crystal structure of the catalytic domain of MMP-13 complexed with WAY-033 | 1ztq | 77.18 |
| 22 | pfd | Crystal structure of the catalytic domain of MMP-13 complexed with a potent pyrimidinetrione inhibitor | 1you | 76.97 |
| 23 | 518 | MMP-13 in complex with a non zinc-chelating inhibitor | 3i7i | 76.64 |
| 24 | la3 | Crystal Structure of Human MMP-13 complexed with an Amino-2-indanol compound | 3ljz | 76.33 |
| 25 | 3w4 | MMP13 IN COMPLEX WITH A NOVEL SELECTIVE NON ZINC BINDING INHIBITOR CMPD22 | 4a7b | 75.78 |
| 26 | 5el | MMP13 in complex with a novel selective non zinc binding inhibitor | 2yig | 75.66 |
| 27 | 732 | MMP-13 in complex with a non zinc-chelating inhibitor | 3i7g | 75.04 |
| 28 | 3w5 | MMP13 IN COMPLEX WITH A NOVEL SELECTIVE NON ZINC BINDING INHIBITOR CMPD22 | 4a7b | 74.85 |
| 29 | 3kr | Crystal structure of MMP-13 in complex with SC-78080 | 3kry | 73.92 |
| 30 | e41 | MMP-13 complexed with 2-Napthylsulfonamide hydroxamic acid inhibitor | 3zxh | 69.37 |
| 31 | 347 | Crystal structure of the catalytic domain of MMP-13 complexed with WAY-344 | 2pjt | 65.66 |