sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.450 Å
X-ray
2014-04-28
| 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: | 23.306 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.423 | 445.500 |
| % Hydrophobic | % Polar |
|---|---|
| 46.21 | 53.79 |
| According to VolSite | |
| HET Code: | CKR |
|---|---|
| Formula: | C15H20N7O2 |
| Molecular weight: | 330.365 g/mol |
| DrugBank ID: | DB07564 |
| Buried Surface Area: | 59.45 % |
| Polar Surface area: | 121.86 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 5 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -16.7676 | 18.8955 | -18.0699 |
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 |
| N22 | OD1 | ASP- 102 | 2.93 | 143.24 | H-Bond (Ligand Donor) |
| N9 | OD2 | ASP- 102 | 2.88 | 172.7 | H-Bond (Ligand Donor) |
| C10 | CB | TYR- 106 | 3.65 | 0 | Hydrophobic |
| N22 | OD1 | ASP- 156 | 2.85 | 156.75 | H-Bond (Ligand Donor) |
| N22 | OD2 | ASP- 156 | 3.5 | 130.87 | H-Bond (Ligand Donor) |
| C4 | SG | CYS- 158 | 3.92 | 0 | Hydrophobic |
| O1 | NE2 | GLN- 203 | 2.97 | 158.99 | H-Bond (Protein Donor) |
| O1 | N | GLY- 230 | 2.79 | 141.24 | H-Bond (Protein Donor) |
| N2 | O | LEU- 231 | 2.91 | 151.69 | H-Bond (Ligand Donor) |
| N14 | O | ALA- 232 | 2.93 | 160.2 | H-Bond (Ligand Donor) |
| C2 | CB | ALA- 232 | 4.43 | 0 | Hydrophobic |
| C10 | CE | MET- 260 | 3.84 | 0 | Hydrophobic |
| C11 | CB | MET- 260 | 4.04 | 0 | Hydrophobic |
| C4 | CB | MET- 260 | 4.04 | 0 | Hydrophobic |
| C2 | CB | ASP- 262 | 3.98 | 0 | Hydrophobic |
| C14 | CB | ASP- 262 | 4.36 | 0 | Hydrophobic |
| C14 | CB | VAL- 282 | 4.47 | 0 | Hydrophobic |
