sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.680 Å
X-ray
2012-09-21
| 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: | 18.767 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.645 | 442.125 |
| % Hydrophobic | % Polar |
|---|---|
| 58.02 | 41.98 |
| According to VolSite | |
| HET Code: | GUN |
|---|---|
| Formula: | C5H5N5O |
| Molecular weight: | 151.126 g/mol |
| DrugBank ID: | DB02377 |
| Buried Surface Area: | 59.71 % |
| Polar Surface area: | 96.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 107.713 | 17.2734 | 21.9792 |
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 |
| N1 | OD2 | ASP- 156 | 2.99 | 172.35 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 156 | 3.07 | 160.77 | H-Bond (Ligand Donor) |
| O6 | NE2 | GLN- 203 | 3.31 | 159.44 | H-Bond (Protein Donor) |
| O6 | N | GLY- 230 | 2.68 | 138.02 | H-Bond (Protein Donor) |
| N2 | O | HOH- 552 | 2.82 | 125.5 | H-Bond (Ligand Donor) |
| N2 | O | HOH- 590 | 2.7 | 128.95 | H-Bond (Ligand Donor) |
