sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2006-04-05
| Name: | Epoxide hydrolase |
|---|---|
| ID: | Q41415_SOLTU |
| AC: | Q41415 |
| Organism: | Solanum tuberosum |
| Reign: | Eukaryota |
| TaxID: | 4113 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 27.370 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.630 | 1073.250 |
| % Hydrophobic | % Polar |
|---|---|
| 58.49 | 41.51 |
| According to VolSite | |
| HET Code: | VPR |
|---|---|
| Formula: | C8H17NO |
| Molecular weight: | 143.227 g/mol |
| DrugBank ID: | DB04165 |
| Buried Surface Area: | 79.47 % |
| Polar Surface area: | 43.09 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 1 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 17.9937 | 92.7966 | 34.1611 |
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 |
| C3A | CD2 | PHE- 33 | 3.52 | 0 | Hydrophobic |
| C5A | CE2 | PHE- 33 | 3.62 | 0 | Hydrophobic |
| N | O | PHE- 33 | 3.17 | 151.18 | H-Bond (Ligand Donor) |
| N | OD1 | ASP- 105 | 3.13 | 153.46 | H-Bond (Ligand Donor) |
| C5A | CD1 | TYR- 154 | 3.97 | 0 | Hydrophobic |
| C4A | CE1 | TYR- 154 | 3.71 | 0 | Hydrophobic |
| C5A | CZ | PHE- 158 | 4.03 | 0 | Hydrophobic |
| C3 | CG2 | ILE- 180 | 3.68 | 0 | Hydrophobic |
| C3A | CG2 | ILE- 180 | 4.29 | 0 | Hydrophobic |
| C5A | CD1 | ILE- 180 | 4.17 | 0 | Hydrophobic |
| C5 | CD2 | TYR- 183 | 4.02 | 0 | Hydrophobic |
| C4A | CD2 | PHE- 189 | 3.45 | 0 | Hydrophobic |
| C5A | CG | PHE- 189 | 4.04 | 0 | Hydrophobic |
| C3 | CE2 | PHE- 189 | 3.9 | 0 | Hydrophobic |
| C2 | CE2 | PHE- 189 | 3.97 | 0 | Hydrophobic |
| C5A | CE2 | PHE- 191 | 4.24 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 266 | 4.44 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 266 | 3.52 | 0 | Hydrophobic |
| C5 | CB | HIS- 300 | 3.89 | 0 | Hydrophobic |
| C5 | CE2 | PHE- 301 | 3.39 | 0 | Hydrophobic |
| C4 | CZ | PHE- 301 | 3.89 | 0 | Hydrophobic |
