sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2002-04-16
| Name: | Biphenyl-2,3-diol 1,2-dioxygenase |
|---|---|
| ID: | BPHC_BURXL |
| AC: | P47228 |
| Organism: | Burkholderia xenovorans |
| Reign: | Bacteria |
| TaxID: | 266265 |
| EC Number: | 1.13.11.39 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 17.655 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | FE2 |
| Ligandability | Volume (Å3) |
|---|---|
| 1.050 | 482.625 |
| % Hydrophobic | % Polar |
|---|---|
| 57.34 | 42.66 |
| According to VolSite | |
| HET Code: | BP3 |
|---|---|
| Formula: | C12H9ClO2 |
| Molecular weight: | 220.652 g/mol |
| DrugBank ID: | DB01925 |
| Buried Surface Area: | 70.47 % |
| Polar Surface area: | 40.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 22.4829 | 22.4109 | 16.7354 |
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 |
| CL1 | CG2 | VAL- 148 | 3.51 | 0 | Hydrophobic |
| CA5 | CD1 | ILE- 173 | 3.87 | 0 | Hydrophobic |
| CA6 | CE | MET- 175 | 4.01 | 0 | Hydrophobic |
| CB2 | CE | MET- 175 | 3.66 | 0 | Hydrophobic |
| CB2 | CE | MET- 175 | 3.66 | 0 | Hydrophobic |
| CL1 | CZ | PHE- 187 | 3.88 | 0 | Hydrophobic |
| CL1 | CB | ALA- 198 | 4.48 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 241 | 3.48 | 0 | Aromatic Face/Face |
| CA4 | CB | HIS- 241 | 4.04 | 0 | Hydrophobic |
| OA2 | OH | TYR- 250 | 2.61 | 158.17 | H-Bond (Protein Donor) |
| CA6 | CB | PRO- 280 | 3.75 | 0 | Hydrophobic |
| CB6 | CB | PRO- 280 | 4.08 | 0 | Hydrophobic |
| OA2 | FE | FE2- 500 | 2.07 | 0 | Metal Acceptor |
| OA3 | FE | FE2- 500 | 2.27 | 0 | Metal Acceptor |
