sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2010-08-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.360 | 5.360 | 5.360 | 0.000 | 5.360 | 1 |
| 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 | 100 % |
| B-Factor: | 99.999 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.574 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 46.51 | 53.49 |
| According to VolSite | |
| HET Code: | Z79 |
|---|---|
| Formula: | C9H12N2O5S |
| Molecular weight: | 260.267 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.16 % |
| Polar Surface area: | 113.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 18.4739 | -12.2326 | -8.289 |
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 |
| O4 | ZN | ZN- 5 | 2.03 | 0 | Metal Acceptor |
| O5 | ZN | ZN- 5 | 2.02 | 0 | Metal Acceptor |
| C7 | CG1 | VAL- 163 | 4.49 | 0 | Hydrophobic |
| O2 | N | LEU- 164 | 2.7 | 154.33 | H-Bond (Protein Donor) |
| C3 | CD1 | LEU- 164 | 4.47 | 0 | Hydrophobic |
| C6 | CB | LEU- 164 | 4.48 | 0 | Hydrophobic |
| N2 | O | ALA- 165 | 2.77 | 163.44 | H-Bond (Ligand Donor) |
| O2 | N | ALA- 165 | 3.33 | 161.88 | H-Bond (Protein Donor) |
| C9 | CG2 | VAL- 198 | 3.96 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 198 | 3.72 | 0 | Hydrophobic |
| C9 | CB | HIS- 201 | 3.95 | 0 | Hydrophobic |
| C4 | CB | HIS- 201 | 3.85 | 0 | Hydrophobic |
| C9 | CD1 | TYR- 223 | 3.66 | 0 | Hydrophobic |
| C2 | CB | TYR- 223 | 4.06 | 0 | Hydrophobic |
