sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 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: | 27.618 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | FE2 |
| Ligandability | Volume (Å3) |
|---|---|
| 0.364 | 307.125 |
| % Hydrophobic | % Polar |
|---|---|
| 56.04 | 43.96 |
| According to VolSite | |
| HET Code: | GTQ |
|---|---|
| Formula: | C7H5O4 |
| Molecular weight: | 153.112 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.44 % |
| Polar Surface area: | 80.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -9.15955 | -25.8755 | -25.7841 |
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 |
| OAA | NE | ARG- 83 | 3.28 | 131.68 | H-Bond (Protein Donor) |
| OAB | NE | ARG- 83 | 2.86 | 148.56 | H-Bond (Protein Donor) |
| OAB | CZ | ARG- 83 | 3.66 | 0 | Ionic (Protein Cationic) |
| CAK | CG | ARG- 83 | 3.79 | 0 | Hydrophobic |
| CAI | CB | ALA- 85 | 4.15 | 0 | Hydrophobic |
| OAC | NE1 | TRP- 104 | 2.86 | 126.27 | H-Bond (Protein Donor) |
| OAA | NE2 | GLN- 108 | 3.01 | 163.35 | H-Bond (Protein Donor) |
| OAA | CZ | ARG- 127 | 3.41 | 0 | Ionic (Protein Cationic) |
| OAA | NE2 | HIS- 162 | 2.84 | 168.12 | H-Bond (Protein Donor) |
| OAC | OD2 | ASP- 174 | 2.63 | 156.6 | H-Bond (Ligand Donor) |
| CAI | CB | ASP- 174 | 3.83 | 0 | Hydrophobic |
| CAF | CD2 | LEU- 176 | 3.66 | 0 | Hydrophobic |
| CAE | CD1 | LEU- 176 | 3.42 | 0 | Hydrophobic |
| CAF | CD1 | ILE- 178 | 3.99 | 0 | Hydrophobic |
| OAB | FE | FE2- 369 | 2.21 | 0 | Metal Acceptor |
| OAD | FE | FE2- 369 | 1.93 | 0 | Metal Acceptor |
