sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.680 Å
X-ray
2016-05-04
| Name: | Envelope glycoprotein |
|---|---|
| ID: | VGP_EBOZM |
| AC: | Q05320 |
| Organism: | Zaire ebolavirus |
| Reign: | Viruses |
| TaxID: | 128952 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 58 % |
| B | 42 % |
| B-Factor: | 60.347 |
|---|---|
| Number of residues: | 19 |
| Including | |
| Standard Amino Acids: | 19 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.272 | 577.125 |
| % Hydrophobic | % Polar |
|---|---|
| 67.25 | 32.75 |
| According to VolSite | |
| HET Code: | IBP |
|---|---|
| Formula: | C13H17O2 |
| Molecular weight: | 205.273 g/mol |
| DrugBank ID: | DB09213 |
| Buried Surface Area: | 43.52 % |
| Polar Surface area: | 40.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -45.7277 | 13.1071 | -6.6528 |
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 |
| O1 | CZ | ARG- 64 | 3.83 | 0 | Ionic (Protein Cationic) |
| C10 | CG2 | VAL- 66 | 4.26 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 184 | 3.7 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 184 | 3.7 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 186 | 4.15 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 186 | 3.84 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 186 | 4.02 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 515 | 3.99 | 0 | Hydrophobic |
| C6 | CE1 | TYR- 517 | 3.76 | 0 | Hydrophobic |
| C7 | CZ | TYR- 517 | 3.42 | 0 | Hydrophobic |
| C5 | CE | MET- 548 | 3.76 | 0 | Hydrophobic |
| C10 | CE | MET- 548 | 3.36 | 0 | Hydrophobic |
| C4 | CB | LEU- 554 | 4.34 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 558 | 3.96 | 0 | Hydrophobic |
