sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2001-01-18
| 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: | 20.468 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.835 | 513.000 |
| % Hydrophobic | % Polar |
|---|---|
| 40.79 | 59.21 |
| According to VolSite | |
| HET Code: | MBS |
|---|---|
| Formula: | C20H20NO6S |
| Molecular weight: | 402.441 g/mol |
| DrugBank ID: | DB04416 |
| Buried Surface Area: | 57.51 % |
| Polar Surface area: | 113.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 1.31414 | 48.9884 | 54.6339 |
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 |
| C5 | CE1 | TYR- 655 | 3.9 | 0 | Hydrophobic |
| O3 | N | LEU- 664 | 2.68 | 163.18 | H-Bond (Protein Donor) |
| C26 | CD1 | LEU- 664 | 4.15 | 0 | Hydrophobic |
| O3 | N | ALA- 665 | 3.39 | 148.73 | H-Bond (Protein Donor) |
| C12 | CB | HIS- 666 | 3.66 | 0 | Hydrophobic |
| C5 | CE2 | TYR- 668 | 4.39 | 0 | Hydrophobic |
| C33 | CB | LEU- 697 | 4.33 | 0 | Hydrophobic |
| C25 | CG1 | VAL- 698 | 4.29 | 0 | Hydrophobic |
| C32 | CG2 | VAL- 698 | 4.37 | 0 | Hydrophobic |
| C32 | CB | HIS- 701 | 3.59 | 0 | Hydrophobic |
| C32 | CB | HIS- 701 | 3.59 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 718 | 4.08 | 0 | Hydrophobic |
| C34 | CD1 | LEU- 718 | 3.9 | 0 | Hydrophobic |
| C6 | CB | TYR- 723 | 4.36 | 0 | Hydrophobic |
| O2 | ZN | ZN- 801 | 1.93 | 0 | Metal Acceptor |
