sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.050 Å
X-ray
1997-07-01
| Name: | Protocatechuate 3,4-dioxygenase beta chain |
|---|---|
| ID: | PCXB_PSEPU |
| AC: | P00437 |
| Organism: | Pseudomonas putida |
| Reign: | Bacteria |
| TaxID: | 303 |
| EC Number: | 1.13.11.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| P | 42 % |
| Q | 58 % |
| B-Factor: | 15.806 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | FE |
| Ligandability | Volume (Å3) |
|---|---|
| 0.392 | 499.500 |
| % Hydrophobic | % Polar |
|---|---|
| 43.92 | 56.08 |
| According to VolSite | |
| HET Code: | CHB |
|---|---|
| Formula: | C7H4ClO3 |
| Molecular weight: | 171.558 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 42.93 % |
| Polar Surface area: | 60.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -20.2801 | -24.8825 | 27.4645 |
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 |
| C2 | CG2 | THR- 12 | 4.46 | 0 | Hydrophobic |
| CL3 | CG2 | THR- 12 | 3.55 | 0 | Hydrophobic |
| C6 | CG | PRO- 15 | 3.74 | 0 | Hydrophobic |
| O1 | OH | TYR- 324 | 2.79 | 165.49 | H-Bond (Protein Donor) |
| C5 | CE2 | TYR- 447 | 3.32 | 0 | Hydrophobic |
| C6 | CB | TRP- 449 | 4.29 | 0 | Hydrophobic |
| O4 | NH1 | ARG- 457 | 3.12 | 142.92 | H-Bond (Protein Donor) |
| C5 | CG | ARG- 457 | 4.13 | 0 | Hydrophobic |
| C4 | CD | ARG- 457 | 4.09 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 491 | 3.47 | 0 | Hydrophobic |
| O4 | FE | FE- 600 | 2.02 | 0 | Metal Acceptor |
