sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2002-10-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.080 | 4.080 | 4.080 | 0.000 | 4.080 | 1 |
| 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: | 32.004 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.550 | 384.750 |
| % Hydrophobic | % Polar |
|---|---|
| 42.98 | 57.02 |
| According to VolSite | |
| HET Code: | BDI |
|---|---|
| Formula: | C9H12N4O2 |
| Molecular weight: | 208.217 g/mol |
| DrugBank ID: | DB02441 |
| Buried Surface Area: | 59.02 % |
| Polar Surface area: | 86.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 16.2287 | 17.4043 | 20.8774 |
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 |
| C6 | CE1 | TYR- 106 | 4.45 | 0 | Hydrophobic |
| C7 | CE2 | TYR- 106 | 3.71 | 0 | Hydrophobic |
| C8 | CZ | TYR- 106 | 3.95 | 0 | Hydrophobic |
| C9 | CE2 | TYR- 106 | 3.86 | 0 | Hydrophobic |
| N5 | OD2 | ASP- 156 | 2.68 | 154.96 | H-Bond (Ligand Donor) |
| N4 | OD1 | ASP- 156 | 2.77 | 133.25 | H-Bond (Ligand Donor) |
| O3 | NE2 | GLN- 203 | 3.22 | 160 | H-Bond (Protein Donor) |
| O3 | N | GLY- 230 | 2.73 | 143.7 | H-Bond (Protein Donor) |
| C6 | CB | ALA- 232 | 4.03 | 0 | Hydrophobic |
| C8 | CB | ALA- 232 | 3.96 | 0 | Hydrophobic |
| C6 | CB | MET- 260 | 4.19 | 0 | Hydrophobic |
| N1 | O | HOH- 1401 | 3.1 | 167.6 | H-Bond (Ligand Donor) |
| O1 | O | HOH- 1404 | 2.63 | 160.61 | H-Bond (Protein Donor) |
