sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2007-02-15
| Name: | Matrix metalloproteinase-9 |
|---|---|
| ID: | MMP9_HUMAN |
| AC: | P14780 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.24.35 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 24.256 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.737 | 513.000 |
| % Hydrophobic | % Polar |
|---|---|
| 36.84 | 63.16 |
| According to VolSite | |
| HET Code: | 6MR |
|---|---|
| Formula: | C23H18IN2O4S |
| Molecular weight: | 545.369 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 49.75 % |
| Polar Surface area: | 110.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 70.0281 | 17.133 | 52.952 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| CB | CG | LEU- 187 | 4.32 | 0 | Hydrophobic |
| OAP | N | LEU- 188 | 2.89 | 151.47 | H-Bond (Protein Donor) |
| CAO | CD1 | LEU- 188 | 4.44 | 0 | Hydrophobic |
| OAP | N | ALA- 189 | 3.16 | 152.36 | H-Bond (Protein Donor) |
| CAK | CG2 | VAL- 398 | 4.28 | 0 | Hydrophobic |
| CAW | CB | HIS- 401 | 4.34 | 0 | Hydrophobic |
| CAK | CB | HIS- 401 | 3.99 | 0 | Hydrophobic |
| OXT | NE2 | GLN- 402 | 3.37 | 131.85 | H-Bond (Protein Donor) |
| CAT | CD1 | LEU- 418 | 4.37 | 0 | Hydrophobic |
| I | CD1 | LEU- 418 | 3.79 | 0 | Hydrophobic |
| CAJ | CD1 | TYR- 423 | 3.33 | 0 | Hydrophobic |
| CAL | CB | TYR- 423 | 3.86 | 0 | Hydrophobic |
| O | ZN | ZN- 444 | 1.92 | 0 | Metal Acceptor |
| OXT | ZN | ZN- 444 | 2.63 | 0 | Metal Acceptor |
| OXT | O | HOH- 545 | 2.6 | 179.96 | H-Bond (Protein Donor) |
