sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
1999-10-07
| 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: | 14.287 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.675 | 573.750 |
| % Hydrophobic | % Polar |
|---|---|
| 45.29 | 54.71 |
| According to VolSite | |
| HET Code: | MM3 |
|---|---|
| Formula: | C15H22N2O5S2 |
| Molecular weight: | 374.476 g/mol |
| DrugBank ID: | DB02350 |
| Buried Surface Area: | 62.41 % |
| Polar Surface area: | 129.62 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -7.0615 | 21.3299 | 28.7862 |
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 |
| S15 | CG2 | VAL- 163 | 3.68 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 163 | 3.73 | 0 | Hydrophobic |
| C6 | CB | LEU- 164 | 4.27 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 164 | 3.9 | 0 | Hydrophobic |
| O11 | N | LEU- 164 | 2.58 | 144.1 | H-Bond (Protein Donor) |
| O11 | N | ALA- 165 | 3.16 | 155.13 | H-Bond (Protein Donor) |
| NA | O | ALA- 165 | 2.84 | 137.32 | H-Bond (Ligand Donor) |
| C20 | CB | HIS- 166 | 4.16 | 0 | Hydrophobic |
| C8 | CG | LEU- 197 | 4.24 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 198 | 4.05 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 198 | 4.5 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 198 | 3.48 | 0 | Hydrophobic |
| C8 | CB | HIS- 201 | 3.64 | 0 | Hydrophobic |
| C4 | CB | HIS- 201 | 4.11 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 218 | 4.48 | 0 | Hydrophobic |
| C18 | CB | PRO- 221 | 4.13 | 0 | Hydrophobic |
| C8 | CD1 | TYR- 223 | 4.07 | 0 | Hydrophobic |
| C2 | CB | TYR- 223 | 3.53 | 0 | Hydrophobic |
| OA | ZN | ZN- 301 | 1.88 | 0 | Metal Acceptor |
| OB | ZN | ZN- 301 | 1.83 | 0 | Metal Acceptor |
