sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.590 Å
X-ray
2011-12-09
| Name: | 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase |
|---|---|
| ID: | BPHD_BURXL |
| AC: | P47229 |
| Organism: | Burkholderia xenovorans |
| Reign: | Bacteria |
| TaxID: | 266265 |
| EC Number: | 3.7.1.8 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 18.414 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.682 | 624.375 |
| % Hydrophobic | % Polar |
|---|---|
| 48.11 | 51.89 |
| According to VolSite | |
| HET Code: | HPK |
|---|---|
| Formula: | C12H9O4 |
| Molecular weight: | 217.197 g/mol |
| DrugBank ID: | DB07911 |
| Buried Surface Area: | 77.11 % |
| Polar Surface area: | 74.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -9.00744 | 16.2069 | -22.232 |
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 |
| OA2 | N | GLY- 41 | 2.82 | 144.6 | H-Bond (Protein Donor) |
| OA3 | N | GLY- 47 | 3.19 | 162.33 | H-Bond (Protein Donor) |
| OA3 | OG | SER- 50 | 2.97 | 136.61 | H-Bond (Protein Donor) |
| CB3 | CD1 | LEU- 172 | 4.21 | 0 | Hydrophobic |
| CB2 | CD2 | LEU- 172 | 3.96 | 0 | Hydrophobic |
| CB4 | CD1 | LEU- 176 | 3.6 | 0 | Hydrophobic |
| CB4 | CB | LEU- 181 | 4.34 | 0 | Hydrophobic |
| CB3 | CG1 | ILE- 182 | 4.45 | 0 | Hydrophobic |
| CB3 | CB | LEU- 186 | 3.47 | 0 | Hydrophobic |
| CB4 | CD1 | LEU- 186 | 3.57 | 0 | Hydrophobic |
| OA4 | NH1 | ARG- 190 | 3.24 | 170.02 | H-Bond (Protein Donor) |
| OA1 | NH1 | ARG- 190 | 2.9 | 147.61 | H-Bond (Protein Donor) |
| OA1 | NH2 | ARG- 190 | 3.41 | 129.38 | H-Bond (Protein Donor) |
| OA1 | CZ | ARG- 190 | 3.57 | 0 | Ionic (Protein Cationic) |
| CB1 | CZ3 | TRP- 266 | 3.43 | 0 | Hydrophobic |
