sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
1998-12-09
| 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: | 11.665 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.907 | 543.375 |
| % Hydrophobic | % Polar |
|---|---|
| 42.86 | 57.14 |
| According to VolSite | |
| HET Code: | S27 |
|---|---|
| Formula: | C20H27N2O3P |
| Molecular weight: | 374.414 g/mol |
| DrugBank ID: | DB08507 |
| Buried Surface Area: | 49.78 % |
| Polar Surface area: | 79.45 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -21.8568 | 28.6731 | -0.317462 |
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 |
| C18 | CG1 | VAL- 163 | 4.3 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 163 | 3.82 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 163 | 3.65 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 164 | 4.2 | 0 | Hydrophobic |
| C9 | CG | LEU- 164 | 3.57 | 0 | Hydrophobic |
| O8 | N | LEU- 164 | 2.74 | 144.7 | H-Bond (Protein Donor) |
| O8 | N | ALA- 165 | 3.19 | 152.12 | H-Bond (Protein Donor) |
| NA | O | ALA- 165 | 3.07 | 152.17 | H-Bond (Ligand Donor) |
| C10 | CB | HIS- 166 | 3.72 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 198 | 3.67 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 201 | 3.98 | 0 | Aromatic Face/Face |
| C4 | CB | HIS- 201 | 3.85 | 0 | Hydrophobic |
| C4 | CB | TYR- 223 | 3.9 | 0 | Hydrophobic |
| OA | ZN | ZN- 301 | 1.88 | 0 | Metal Acceptor |
| OB | ZN | ZN- 301 | 2.01 | 0 | Metal Acceptor |
