sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.880 Å
X-ray
2012-07-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.880 | 6.880 | 6.880 | 0.000 | 6.880 | 2 |
| 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: | 24.448 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.862 | 607.500 |
| % Hydrophobic | % Polar |
|---|---|
| 42.22 | 57.78 |
| According to VolSite | |
| HET Code: | NGH |
|---|---|
| Formula: | C13H20N2O5S |
| Molecular weight: | 316.373 g/mol |
| DrugBank ID: | DB08271 |
| Buried Surface Area: | 59.27 % |
| Polar Surface area: | 104.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 21.3605 | 68.8831 | 106.078 |
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 |
| C10 | CG2 | VAL- 163 | 4.44 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 163 | 4 | 0 | Hydrophobic |
| C5 | CB | LEU- 164 | 4.1 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 164 | 4.22 | 0 | Hydrophobic |
| O2 | N | LEU- 164 | 2.62 | 167.77 | H-Bond (Protein Donor) |
| N1 | O | ALA- 165 | 2.95 | 166.36 | H-Bond (Ligand Donor) |
| C3 | CG2 | VAL- 198 | 4.1 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 198 | 3.8 | 0 | Hydrophobic |
| C7 | CB | HIS- 201 | 3.51 | 0 | Hydrophobic |
| C3 | CB | HIS- 201 | 3.9 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 218 | 4.31 | 0 | Hydrophobic |
| C13 | CB | PRO- 221 | 4.28 | 0 | Hydrophobic |
| C7 | CD1 | TYR- 223 | 4.33 | 0 | Hydrophobic |
| C2 | CB | TYR- 223 | 3.99 | 0 | Hydrophobic |
| O4 | ZN | ZN- 302 | 2.27 | 0 | Metal Acceptor |
| O5 | ZN | ZN- 302 | 2.26 | 0 | Metal Acceptor |
