sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.440 Å
X-ray
1999-10-25
| 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: | 9.390 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.650 | 607.500 |
| % Hydrophobic | % Polar |
|---|---|
| 44.44 | 55.56 |
| According to VolSite | |
| HET Code: | BBH |
|---|---|
| Formula: | C19H21N3O6S |
| Molecular weight: | 419.452 g/mol |
| DrugBank ID: | DB04140 |
| Buried Surface Area: | 49.76 % |
| Polar Surface area: | 124.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 3.70803 | 50.1473 | 53.4362 |
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 |
| C1 | CD1 | LEU- 664 | 4.27 | 0 | Hydrophobic |
| C6 | CB | LEU- 664 | 4.43 | 0 | Hydrophobic |
| O10 | N | LEU- 664 | 2.79 | 163.42 | H-Bond (Protein Donor) |
| O10 | N | ALA- 665 | 3.36 | 155.81 | H-Bond (Protein Donor) |
| NA | O | ALA- 665 | 3.13 | 151.29 | H-Bond (Ligand Donor) |
| C5 | CG1 | VAL- 698 | 3.57 | 0 | Hydrophobic |
| C8 | CB | HIS- 701 | 3.63 | 0 | Hydrophobic |
| C4 | CB | HIS- 701 | 3.9 | 0 | Hydrophobic |
| OA | OE2 | GLU- 702 | 2.62 | 176.15 | H-Bond (Protein Donor) |
| C8 | CD1 | LEU- 718 | 4.2 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 722 | 3.68 | 0 | Hydrophobic |
| C8 | CD1 | TYR- 723 | 4.29 | 0 | Hydrophobic |
| C3 | CB | TYR- 723 | 3.89 | 0 | Hydrophobic |
| OA | ZN | ZN- 801 | 1.83 | 0 | Metal Acceptor |
| OB | ZN | ZN- 801 | 1.97 | 0 | Metal Acceptor |
