| Index | Ligand Name | Ligand Structure | Gene Name Primary | Protein Name | Uniprot ID | Gene Name Synonym | PDB Codes |
| 1 | rs2 | | MMP1 | Interstitial collagenase | P03956 | CLG | 966c |
| 2 | ngh | | MMP10,MMP12 | Stromelysin-2 | P09238 | STMY2 | 1q3a, 1rmz, 5lab |
| 3 | hs5 | | MMP12 | Macrophage metalloelastase | P39900 | HME | 3f18 |
| 4 | deo | | MMP12 | Macrophage metalloelastase | P39900 | HME | 1ros |
| 5 | b9n | | MMP12 | Macrophage metalloelastase | P39900 | HME | 6ekn |
| 6 | cp8 | | MMP12 | Macrophage metalloelastase | P39900 | HME | 1utt |
| 7 | 576 | | MMP12 | Macrophage metalloelastase | P39900 | HME | 2woa |
| 8 | cgs | | MMP12 | Macrophage metalloelastase | P39900 | HME | 1jiz, 2w0d |
| 9 | jt5 | | MMP12 | Macrophage metalloelastase | P39900 | HME | 3n2v |
| 10 | nhk | | MMP12 | Macrophage metalloelastase | P39900 | HME | 3nx7 |
| 11 | 0d2 | | MMP12 | Macrophage metalloelastase | P39900 | HME | 3uvc |
| 12 | e37 | | MMP12 | Macrophage metalloelastase | P39900 | HME | 4efs |
| 13 | y38 | | MMP12 | Macrophage metalloelastase | P39900 | HME | 4h84 |
| 14 | lpw | | MMP12 | Macrophage metalloelastase | P39900 | HME | 6enm |
| 15 | z79 | | MMP12,MMP3 | Macrophage metalloelastase | P39900 | HME | 3lk8, 3oho |
| 16 | b9z | | MMP12,MMP9 | Macrophage metalloelastase | P39900 | HME | 6ela, 6esm |
| 17 | 10b | | MMP12,MMP9 | Macrophage metalloelastase | P39900 | HME | 4h3x, 4h76 |
| 18 | az6 | | MMP13 | Collagenase 3 | P45452 | | 4jpa |
| 19 | az4 | | MMP13 | Collagenase 3 | P45452 | | 4jp4 |
| 20 | 8om | | MMP13 | Collagenase 3 | P45452 | | 5uwk |
| 21 | 518 | | MMP13 | Collagenase 3 | P45452 | | 3i7i |
| 22 | 3kr | | MMP13 | Collagenase 3 | P45452 | | 3kry |
| 23 | 24f | | MMP13 | Collagenase 3 | P45452 | | 3elm |
| 24 | 033 | | MMP13 | Collagenase 3 | P45452 | | 1ztq |
| 25 | pb3 | | MMP13 | Collagenase 3 | P45452 | | 1xuc |
| 26 | pb4 | | MMP13 | Collagenase 3 | P45452 | | 1xud |
| 27 | pb5 | | MMP13 | Collagenase 3 | P45452 | | 1xur |
| 28 | pfd | | MMP13 | Collagenase 3 | P45452 | | 1you |
| 29 | gg1 | | MMP13 | Collagenase 3 | P45452 | | 2ozr |
| 30 | 347 | | MMP13 | Collagenase 3 | P45452 | | 2pjt |
| 31 | 5el | | MMP13 | Collagenase 3 | P45452 | | 2yig |
| 32 | 732 | | MMP13 | Collagenase 3 | P45452 | | 3i7g |
| 33 | 3ke | | MMP13 | Collagenase 3 | P45452 | | 3kec |
| 34 | 3ej | | MMP13 | Collagenase 3 | P45452 | | 3kej |
| 35 | 3ek | | MMP13 | Collagenase 3 | P45452 | | 3kek |
| 36 | la3 | | MMP13 | Collagenase 3 | P45452 | | 3ljz |
| 37 | whh | | MMP13 | Collagenase 3 | P45452 | | 3wv1 |
| 38 | wgg | | MMP13 | Collagenase 3 | P45452 | | 3wv2 |
| 39 | wll | | MMP13 | Collagenase 3 | P45452 | | 3wv3 |
| 40 | e41 | | MMP13 | Collagenase 3 | P45452 | | 3zxh |
| 41 | cbp | | MMP13 | Collagenase 3 | P45452 | | 1cxv, 456c |
| 42 | 3w4 | | MMP13 | Collagenase 3 | P45452 | | 4a7b |
| 43 | 3w5 | | MMP13 | Collagenase 3 | P45452 | | 4a7b |
| 44 | wnn | | MMP13 | Collagenase 3 | P45452 | | 5b5p |
| 45 | 4uf | | MMP13 | Collagenase 3 | P45452 | | 5bpa |
| 46 | 8oj | | MMP13 | Collagenase 3 | P45452 | | 5uwl |
| 47 | rs1 | | MMP13 | Collagenase 3 | P45452 | | 830c |
| 48 | spc | | MMP3 | Stromelysin-1 | P08254 | STMY1 | 1d7x |
| 49 | n25 | | MMP3 | Stromelysin-1 | P08254 | STMY1 | 1bqo |
| 50 | in7 | | MMP3 | Stromelysin-1 | P08254 | STMY1 | 1b8y |
| 51 | s80 | | MMP3 | Stromelysin-1 | P08254 | STMY1 | 1biw |
| 52 | mm3 | | MMP3 | Stromelysin-1 | P08254 | STMY1 | 1d5j |
| 53 | hqq | | MMP3 | Stromelysin-1 | P08254 | STMY1 | 1g4k |
| 54 | in9 | | MMP3 | Stromelysin-1 | P08254 | STMY1 | 1usn |
| 55 | ohl | | MMP3 | Stromelysin-1 | P08254 | STMY1 | 3ohl |
| 56 | tqj | | MMP7 | Matrilysin | P09237 | MPSL1 PUMP1 | 2y6d |
| 57 | rss | | MMP7 | Matrilysin | P09237 | MPSL1 PUMP1 | 1mmp |
| 58 | rrs | | MMP7 | Matrilysin | P09237 | MPSL1 PUMP1 | 1mmq |
| 59 | srs | | MMP7 | Matrilysin | P09237 | MPSL1 PUMP1 | 1mmr |
| 60 | axb | | MMP8 | Neutrophil collagenase | P22894 | CLG1 | 3dpe, 3dpf |
| 61 | bsi | | MMP8 | Neutrophil collagenase | P22894 | CLG1 | 1bzs, 1i76 |
| 62 | bbt | | MMP8 | Neutrophil collagenase | P22894 | CLG1 | 1jj9 |
| 63 | 2ni | | MMP8 | Neutrophil collagenase | P22894 | CLG1 | 1zp5 |
| 64 | axa | | MMP8 | Neutrophil collagenase | P22894 | CLG1 | 3dng |
| 65 | e40 | | MMP9 | Matrix metalloproteinase-9 | P14780 | CLG4B | 4wzv |