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
1999-02-03
| Name: | Stromelysin-1 |
|---|---|
| ID: | MMP3_HUMAN |
| AC: | P08254 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.24.17 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 19.340 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.921 | 668.250 |
| % Hydrophobic | % Polar |
|---|---|
| 47.47 | 52.53 |
| According to VolSite | |
| HET Code: | IN7 |
|---|---|
| Formula: | C19H21N2O4S |
| Molecular weight: | 373.446 g/mol |
| DrugBank ID: | DB07986 |
| Buried Surface Area: | 70.55 % |
| Polar Surface area: | 97.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 16.4797 | 8.45838 | 18.4657 |
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 |
| C3 | CD1 | LEU- 164 | 4.47 | 0 | Hydrophobic |
| O1 | N | LEU- 164 | 2.81 | 155.56 | H-Bond (Protein Donor) |
| C13 | CB | LEU- 197 | 3.9 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 197 | 3.82 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 197 | 3.9 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 198 | 4.17 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 198 | 4.34 | 0 | Hydrophobic |
| C15 | CB | HIS- 201 | 3.7 | 0 | Hydrophobic |
| C2 | CB | HIS- 201 | 4.38 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 218 | 4.09 | 0 | Hydrophobic |
| C15 | CD1 | TYR- 223 | 3.86 | 0 | Hydrophobic |
| C1 | CB | TYR- 223 | 3.94 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 226 | 4.08 | 0 | Hydrophobic |
| C12 | CG | LEU- 226 | 3.98 | 0 | Hydrophobic |
| O4 | ZN | ZN- 301 | 2.02 | 0 | Metal Acceptor |
