sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2010-06-21
| Name: | Gentisate 1,2-dioxygenase |
|---|---|
| ID: | Q67FT0_PSESE |
| AC: | Q67FT0 |
| Organism: | Pseudaminobacter salicylatoxidans |
| Reign: | Bacteria |
| TaxID: | 93369 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 37.043 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | FE2 |
| Ligandability | Volume (Å3) |
|---|---|
| 0.527 | 340.875 |
| % Hydrophobic | % Polar |
|---|---|
| 60.40 | 39.60 |
| According to VolSite | |
| HET Code: | 1HN |
|---|---|
| Formula: | C11H7O3 |
| Molecular weight: | 187.171 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 72.96 % |
| Polar Surface area: | 60.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -9.12136 | -26.3016 | -26.0731 |
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 |
| O2 | NE | ARG- 83 | 3.31 | 140.61 | H-Bond (Protein Donor) |
| O3 | NH2 | ARG- 83 | 3.47 | 126.19 | H-Bond (Protein Donor) |
| O3 | NE | ARG- 83 | 2.89 | 148.47 | H-Bond (Protein Donor) |
| O3 | CZ | ARG- 83 | 3.59 | 0 | Ionic (Protein Cationic) |
| C2 | CG | ARG- 83 | 3.73 | 0 | Hydrophobic |
| C4 | CB | ALA- 85 | 4.13 | 0 | Hydrophobic |
| C5 | CE2 | TRP- 104 | 3.48 | 0 | Hydrophobic |
| O2 | NE2 | GLN- 108 | 3.16 | 169.04 | H-Bond (Protein Donor) |
| O2 | CZ | ARG- 127 | 3.31 | 0 | Ionic (Protein Cationic) |
| O2 | NE2 | HIS- 162 | 2.6 | 153.88 | H-Bond (Protein Donor) |
| C4 | CB | ASP- 174 | 3.93 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 176 | 3.85 | 0 | Hydrophobic |
| C4A | CD1 | LEU- 176 | 3.71 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 176 | 3.53 | 0 | Hydrophobic |
| C7 | CG1 | ILE- 178 | 3.25 | 0 | Hydrophobic |
| O3 | FE | FE2- 369 | 2.32 | 0 | Metal Acceptor |
