Table 3. Binding interactions of MMP-1 (PDB: 966C), MMP-3 (PDB: 1G4K) and MMP-9 (PDB: 2OW0) and the co-crystallized ligands in the experimental structures (before docking) and after molecular docking
| Protein\Ligand | Experimental structure | After docking |
| MMP-1 (PDB: 966C) | Hydroxamic-Ala182 | Hydroxamic-Ala182 |
| Hydroxamic-Glu219 | Hydroxamic-Glu219 |
| Hydroxamic-Zn2+ | Hydroxamic-Zn2+ |
| Sulfone-Leu181 | Sulfone-Leu181 |
| MMP-3 (PDB: 1G4K) | Pyrimidine (O2)-Leu164 | Pyrimidine (O4)-Leu164 |
| Pyrimidine (N1)-Ala165 | Pyrimidine (N3)-Ala165 |
| Pyrimidine-H2O-Glu202 | Pyrimidine-His211 |
| Pyrimidine-H2O-Ala167 | Phenol-His224 |
| Pyrimidine (N2)-Zn2+ | Pyrimidine (O2)-Zn2+ |
| Phenoxy-His201 | |
| MMP-9 (PDB: 2OW0) | Carboxyl-Zn2+ | Carboxyl-Zn2+ |
| Carboxyl-His411 | Carboxyl-Gln402 |
| Carboxyl-Gln402 | Sulfone-Ala189 |
| Sulfone-Ala189 | Sulfone-Leu188 |
| Sulfone-Leu188 | |