sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2003-11-27
| Name: | Matrix metalloproteinase-16 |
|---|---|
| ID: | MMP16_HUMAN |
| AC: | P51512 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.24 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.518 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.056 | 259.875 |
| % Hydrophobic | % Polar |
|---|---|
| 41.56 | 58.44 |
| According to VolSite | |
| HET Code: | BAT |
|---|---|
| Formula: | C23H31N3O4S2 |
| Molecular weight: | 477.640 g/mol |
| DrugBank ID: | DB03880 |
| Buried Surface Area: | 49.12 % |
| Polar Surface area: | 161.07 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 0.524031 | 2.93537 | 48.0162 |
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 |
| N3 | O | GLY- 204 | 2.98 | 157.1 | H-Bond (Ligand Donor) |
| S1 | CB | PHE- 205 | 3.95 | 0 | Hydrophobic |
| C3 | CB | PHE- 205 | 4.11 | 0 | Hydrophobic |
| C22 | CB | PHE- 205 | 4.13 | 0 | Hydrophobic |
| O3 | N | LEU- 206 | 2.79 | 154.39 | H-Bond (Protein Donor) |
| C12 | CD1 | LEU- 206 | 4.06 | 0 | Hydrophobic |
| N1 | O | ALA- 207 | 2.91 | 172.96 | H-Bond (Ligand Donor) |
| C12 | CG2 | VAL- 243 | 3.83 | 0 | Hydrophobic |
| O2 | OE1 | GLU- 247 | 2.67 | 159.17 | H-Bond (Protein Donor) |
| N2 | O | PRO- 266 | 2.96 | 163.78 | H-Bond (Ligand Donor) |
| C17 | CD2 | PHE- 267 | 3.82 | 0 | Hydrophobic |
| O4 | N | TYR- 268 | 2.81 | 160.76 | H-Bond (Protein Donor) |
| C10 | CB | TYR- 268 | 4.4 | 0 | Hydrophobic |
| O1 | ZN | ZN- 500 | 1.87 | 0 | Metal Acceptor |
| O2 | ZN | ZN- 500 | 2.24 | 0 | Metal Acceptor |
