sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2005-01-28
| Name: | Collagenase 3 |
|---|---|
| ID: | MMP13_HUMAN |
| AC: | P45452 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.24 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 96 % |
| B | 4 % |
| B-Factor: | 19.110 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.874 | 465.750 |
| % Hydrophobic | % Polar |
|---|---|
| 42.03 | 57.97 |
| According to VolSite | |
| HET Code: | PFD |
|---|---|
| Formula: | C20H19FN2O6 |
| Molecular weight: | 402.373 g/mol |
| DrugBank ID: | DB08388 |
| Buried Surface Area: | 62.13 % |
| Polar Surface area: | 102.96 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 42.8363 | 36.3782 | -2.83883 |
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 |
| C11 | CD1 | LEU- 184 | 4.1 | 0 | Hydrophobic |
| C13 | CB | LEU- 185 | 4.19 | 0 | Hydrophobic |
| C6 | CG | LEU- 185 | 4.09 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 185 | 4.09 | 0 | Hydrophobic |
| O8 | N | LEU- 185 | 2.82 | 179.2 | H-Bond (Protein Donor) |
| O8 | N | ALA- 186 | 3.46 | 165.29 | H-Bond (Protein Donor) |
| C24 | CB | LEU- 218 | 4.15 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 219 | 4.27 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 219 | 3.86 | 0 | Hydrophobic |
| C23 | CB | HIS- 222 | 3.79 | 0 | Hydrophobic |
| C17 | CB | HIS- 222 | 4.13 | 0 | Hydrophobic |
| C28 | CD1 | LEU- 239 | 4.18 | 0 | Hydrophobic |
| C16 | CB | TYR- 244 | 3.97 | 0 | Hydrophobic |
| F29 | CB | THR- 245 | 3.98 | 0 | Hydrophobic |
| N9 | ZN | ZN- 301 | 2.11 | 0 | Metal Acceptor |
