sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.960 Å
X-ray
2012-02-13
| 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: | 29.231 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.811 | 621.000 |
| % Hydrophobic | % Polar |
|---|---|
| 41.85 | 58.15 |
| According to VolSite | |
| HET Code: | NGH |
|---|---|
| Formula: | C13H20N2O5S |
| Molecular weight: | 316.373 g/mol |
| DrugBank ID: | DB08271 |
| Buried Surface Area: | 58.97 % |
| 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 |
|---|---|---|
| 2.80467 | -9.79362 | -0.784667 |
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 | CG1 | VAL- 163 | 4.37 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 163 | 4.11 | 0 | Hydrophobic |
| C1 | CB | LEU- 164 | 4.34 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 164 | 4.07 | 0 | Hydrophobic |
| O2 | N | ALA- 165 | 3.34 | 143.36 | H-Bond (Protein Donor) |
| N1 | O | ALA- 165 | 2.84 | 165.52 | H-Bond (Ligand Donor) |
| C3 | CG2 | VAL- 198 | 4.23 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 198 | 3.79 | 0 | Hydrophobic |
| C7 | CB | HIS- 201 | 3.42 | 0 | Hydrophobic |
| C3 | CB | HIS- 201 | 3.91 | 0 | Hydrophobic |
| O4 | OE2 | GLU- 202 | 2.62 | 168.74 | H-Bond (Protein Donor) |
| C7 | CD1 | LEU- 218 | 4.13 | 0 | Hydrophobic |
| C9 | CB | PRO- 221 | 4.34 | 0 | Hydrophobic |
| C13 | CB | PRO- 221 | 4.34 | 0 | Hydrophobic |
| C4 | CB | TYR- 223 | 3.67 | 0 | Hydrophobic |
| O4 | ZN | ZN- 301 | 2.35 | 0 | Metal Acceptor |
| O5 | ZN | ZN- 301 | 2.2 | 0 | Metal Acceptor |
