sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2000-06-02
| Name: | Queuine tRNA-ribosyltransferase |
|---|---|
| ID: | TGT_ZYMMO |
| AC: | P28720 |
| Organism: | Zymomonas mobilis subsp. mobilis |
| Reign: | Bacteria |
| TaxID: | 264203 |
| EC Number: | 2.4.2.29 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.841 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.520 | 415.125 |
| % Hydrophobic | % Polar |
|---|---|
| 52.85 | 47.15 |
| According to VolSite | |
| HET Code: | DPZ |
|---|---|
| Formula: | C8H8N4O2 |
| Molecular weight: | 192.175 g/mol |
| DrugBank ID: | DB04169 |
| Buried Surface Area: | 68.21 % |
| Polar Surface area: | 110.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 17.0144 | 17.2299 | 21.9191 |
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 |
| C4 | CB | TYR- 106 | 3.89 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 156 | 3.04 | 125.19 | H-Bond (Ligand Donor) |
| N12 | OD2 | ASP- 156 | 2.72 | 158.17 | H-Bond (Ligand Donor) |
| C8 | SG | CYS- 158 | 3.96 | 0 | Hydrophobic |
| O11 | NE2 | GLN- 203 | 2.96 | 157.74 | H-Bond (Protein Donor) |
| O11 | N | GLY- 230 | 2.63 | 139.49 | H-Bond (Protein Donor) |
| N13 | O | LEU- 231 | 2.83 | 152.97 | H-Bond (Ligand Donor) |
| C4 | SD | MET- 260 | 3.99 | 0 | Hydrophobic |
| C6 | CB | MET- 260 | 3.89 | 0 | Hydrophobic |
| O3 | O | HOH- 945 | 2.78 | 168.61 | H-Bond (Protein Donor) |
