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
1999-10-20
| 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 | 79 % |
| B | 21 % |
| B-Factor: | 11.371 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.976 | 668.250 |
| % Hydrophobic | % Polar |
|---|---|
| 40.91 | 59.09 |
| According to VolSite | |
| HET Code: | SPC |
|---|---|
| Formula: | C13H19N3O6S |
| Molecular weight: | 345.371 g/mol |
| DrugBank ID: | DB01877 |
| Buried Surface Area: | 69.16 % |
| Polar Surface area: | 125.58 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -7.07422 | 20.7662 | 27.9828 |
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 |
| O12 | N | LEU- 164 | 2.65 | 163.26 | H-Bond (Protein Donor) |
| C1 | CD1 | LEU- 164 | 4.04 | 0 | Hydrophobic |
| O12 | N | ALA- 165 | 3.43 | 149.29 | H-Bond (Protein Donor) |
| N32 | O | ALA- 165 | 2.93 | 144.97 | H-Bond (Ligand Donor) |
| C8 | CG | LEU- 197 | 4.4 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 198 | 4.39 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 198 | 3.73 | 0 | Hydrophobic |
| C8 | CB | HIS- 201 | 3.56 | 0 | Hydrophobic |
| C4 | CB | HIS- 201 | 3.87 | 0 | Hydrophobic |
| O33 | OE2 | GLU- 202 | 2.79 | 153.25 | H-Bond (Protein Donor) |
| C8 | CD1 | LEU- 218 | 4.47 | 0 | Hydrophobic |
| C18 | CB | PRO- 221 | 3.98 | 0 | Hydrophobic |
| C25 | CB | PRO- 221 | 4.12 | 0 | Hydrophobic |
| C3 | CB | TYR- 223 | 4.1 | 0 | Hydrophobic |
| C25 | CG | GLN- 736 | 4.05 | 0 | Hydrophobic |
