sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
1999-10-22
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 6.806 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.618 | 546.750 |
| % Hydrophobic | % Polar |
|---|---|
| 43.83 | 56.17 |
| According to VolSite | |
| HET Code: | SPI |
|---|---|
| Formula: | C20H23N3O7S |
| Molecular weight: | 449.478 g/mol |
| DrugBank ID: | DB04232 |
| Buried Surface Area: | 45.5 % |
| Polar Surface area: | 133.86 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 1.75613 | 51.1251 | 53.1771 |
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 |
| O1 | N | LEU- 664 | 2.89 | 145.18 | H-Bond (Protein Donor) |
| C1 | CD1 | LEU- 664 | 4.43 | 0 | Hydrophobic |
| O1 | N | ALA- 665 | 3.22 | 152.71 | H-Bond (Protein Donor) |
| NA | O | ALA- 665 | 3.28 | 166.24 | H-Bond (Ligand Donor) |
| C4 | CG2 | VAL- 698 | 4.36 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 698 | 3.48 | 0 | Hydrophobic |
| C7 | CB | HIS- 701 | 4.06 | 0 | Hydrophobic |
| C5 | CB | HIS- 701 | 3.7 | 0 | Hydrophobic |
| OA | OE2 | GLU- 702 | 3 | 159.4 | H-Bond (Protein Donor) |
| C7 | CD1 | LEU- 718 | 4.25 | 0 | Hydrophobic |
| C7 | CD1 | TYR- 723 | 4.04 | 0 | Hydrophobic |
| C3 | CB | TYR- 723 | 3.61 | 0 | Hydrophobic |
| OA | ZN | ZN- 801 | 1.85 | 0 | Metal Acceptor |
| OB | ZN | ZN- 801 | 2.33 | 0 | Metal Acceptor |
