sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2014-05-02
| Name: | D-tagatose 3-epimerase |
|---|---|
| ID: | DT3E_PSECI |
| AC: | O50580 |
| Organism: | Pseudomonas cichorii |
| Reign: | Bacteria |
| TaxID: | 36746 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 20.586 |
|---|---|
| Number of residues: | 18 |
| Including | |
| Standard Amino Acids: | 17 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.102 | 249.750 |
| % Hydrophobic | % Polar |
|---|---|
| 39.19 | 60.81 |
| According to VolSite | |
| HET Code: | SOE |
|---|---|
| Formula: | C6H12O6 |
| Molecular weight: | 180.156 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.33 % |
| Polar Surface area: | 110.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 5 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 68.9421 | 2.73383 | 35.9442 |
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 | CE | MET- 121 | 3.98 | 0 | Hydrophobic |
| C6 | CE | MET- 121 | 3.55 | 0 | Hydrophobic |
| O4 | O | VAL- 122 | 2.83 | 163.85 | H-Bond (Ligand Donor) |
| O5 | N | LYS- 124 | 3.17 | 147.87 | H-Bond (Protein Donor) |
| C3 | CB | THR- 251 | 4.14 | 0 | Hydrophobic |
| C5 | CB | THR- 251 | 4.49 | 0 | Hydrophobic |
| O1 | N | GLY- 252 | 2.96 | 164.66 | H-Bond (Protein Donor) |
| O3 | O | GLY- 252 | 2.73 | 156.75 | H-Bond (Ligand Donor) |
| C1 | CB | SER- 256 | 3.92 | 0 | Hydrophobic |
| C1 | CG | ARG- 257 | 4.38 | 0 | Hydrophobic |
| O1 | O | VAL- 261 | 2.73 | 173.6 | H-Bond (Ligand Donor) |
| C6 | CB | TRP- 262 | 4.23 | 0 | Hydrophobic |
| C1 | CE3 | TRP- 262 | 3.89 | 0 | Hydrophobic |
