sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2007-03-27
| Name: | TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase |
|---|---|
| ID: | FDTA_ANETH |
| AC: | Q6T1W8 |
| Organism: | Aneurinibacillus thermoaerophilus |
| Reign: | Bacteria |
| TaxID: | 143495 |
| EC Number: | 5.3.2.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 55 % |
| B | 45 % |
| B-Factor: | 24.519 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.380 | 489.375 |
| % Hydrophobic | % Polar |
|---|---|
| 41.38 | 58.62 |
| According to VolSite | |
| HET Code: | TYD |
|---|---|
| Formula: | C10H13N2O11P2 |
| Molecular weight: | 399.165 g/mol |
| DrugBank ID: | DB03103 |
| Buried Surface Area: | 41.83 % |
| Polar Surface area: | 220.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -7.32576 | 13.7509 | 8.47524 |
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 |
| C1' | CG1 | ILE- 11 | 4.2 | 0 | Hydrophobic |
| C4' | CG2 | ILE- 11 | 3.96 | 0 | Hydrophobic |
| O2A | NH2 | ARG- 15 | 3.29 | 140.12 | H-Bond (Protein Donor) |
| O1B | NH2 | ARG- 15 | 3.44 | 125.42 | H-Bond (Protein Donor) |
| O2B | NH1 | ARG- 15 | 3.08 | 158.66 | H-Bond (Protein Donor) |
| O2B | CZ | ARG- 15 | 3.75 | 0 | Ionic (Protein Cationic) |
| C5M | CD1 | LEU- 18 | 4 | 0 | Hydrophobic |
| O4 | NH2 | ARG- 33 | 2.81 | 147.83 | H-Bond (Protein Donor) |
| C5M | CE2 | TYR- 35 | 4.15 | 0 | Hydrophobic |
| C5M | CD1 | TYR- 114 | 4.14 | 0 | Hydrophobic |
| C2' | CZ | TYR- 114 | 3.42 | 0 | Hydrophobic |
| O3B | CZ | ARG- 121 | 3.95 | 0 | Ionic (Protein Cationic) |
| O3B | NH1 | ARG- 121 | 2.9 | 121.86 | H-Bond (Protein Donor) |
