sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.420 Å
X-ray
2012-07-31
| 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: | 14.509 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.423 | 411.750 |
| % Hydrophobic | % Polar |
|---|---|
| 50.82 | 49.18 |
| According to VolSite | |
| HET Code: | PRF |
|---|---|
| Formula: | C7H10N5O |
| Molecular weight: | 180.187 g/mol |
| DrugBank ID: | DB03304 |
| Buried Surface Area: | 69.85 % |
| Polar Surface area: | 110.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 17.0682 | 16.9342 | 21.7632 |
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 | 2.82 | 175.54 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 156 | 2.82 | 152.48 | H-Bond (Ligand Donor) |
| O6 | NE2 | GLN- 203 | 3.21 | 153.7 | H-Bond (Protein Donor) |
| O6 | N | GLY- 230 | 2.91 | 136.75 | H-Bond (Protein Donor) |
| N11 | O | LEU- 231 | 2.82 | 164.46 | H-Bond (Ligand Donor) |
| N11 | O | MET- 260 | 2.88 | 159.12 | H-Bond (Ligand Donor) |
