sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.450 Å
X-ray
2002-01-28
| Name: | Biphenyl-2,3-diol 1,2-dioxygenase |
|---|---|
| ID: | BPHC_PSES1 |
| AC: | P17297 |
| Organism: | Pseudomonas sp. |
| Reign: | Bacteria |
| TaxID: | 307 |
| EC Number: | 1.13.11.39 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 9.417 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | FE2 |
| Ligandability | Volume (Å3) |
|---|---|
| 0.994 | 384.750 |
| % Hydrophobic | % Polar |
|---|---|
| 50.88 | 49.12 |
| According to VolSite | |
| HET Code: | BPY |
|---|---|
| Formula: | C12H10O2 |
| Molecular weight: | 186.207 g/mol |
| DrugBank ID: | DB02923 |
| Buried Surface Area: | 75.25 % |
| 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 |
|---|---|---|
| 83.3106 | 38.6635 | 16.5451 |
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 |
| CK8 | CG2 | VAL- 147 | 4.08 | 0 | Hydrophobic |
| CK9 | CG1 | VAL- 147 | 4.37 | 0 | Hydrophobic |
| CK6 | CD1 | ILE- 172 | 3.72 | 0 | Hydrophobic |
| CK9 | CD1 | ILE- 174 | 3.95 | 0 | Hydrophobic |
| OK1 | NE2 | HIS- 194 | 2.6 | 158.07 | H-Bond (Protein Donor) |
| DuAr | DuAr | HIS- 240 | 3.46 | 0 | Aromatic Face/Face |
| CK5 | CB | HIS- 240 | 4.1 | 0 | Hydrophobic |
| OK2 | OH | TYR- 249 | 2.72 | 162.82 | H-Bond (Protein Donor) |
| CK1 | CB | THR- 280 | 3.81 | 0 | Hydrophobic |
| CKC | CG2 | THR- 280 | 3.64 | 0 | Hydrophobic |
| OK1 | FE | FE2- 301 | 2.3 | 0 | Metal Acceptor |
| OK2 | FE | FE2- 301 | 1.98 | 0 | Metal Acceptor |
