sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2000-04-19
| Name: | Glutamine--tRNA ligase |
|---|---|
| ID: | SYQ_ECOLI |
| AC: | P00962 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 6.1.1.18 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 19.593 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.279 | 658.125 |
| % Hydrophobic | % Polar |
|---|---|
| 42.56 | 57.44 |
| According to VolSite | |
| HET Code: | QSI |
|---|---|
| Formula: | C15H22N8O8S |
| Molecular weight: | 474.449 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.92 % |
| Polar Surface area: | 272.95 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 41.8723 | 28.7039 | 15.9193 |
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 |
| C1' | CE1 | PHE- 31 | 4.39 | 0 | Hydrophobic |
| C4' | CE1 | PHE- 31 | 3.86 | 0 | Hydrophobic |
| N | O | PRO- 32 | 3.28 | 161.23 | H-Bond (Ligand Donor) |
| CB | CG | PRO- 32 | 4.02 | 0 | Hydrophobic |
| C5' | CB | PRO- 33 | 4.02 | 0 | Hydrophobic |
| O2S | N | GLU- 34 | 2.97 | 149.02 | H-Bond (Protein Donor) |
| O5' | NE2 | HIS- 43 | 3.49 | 132.8 | H-Bond (Protein Donor) |
| O2' | OG | SER- 46 | 2.79 | 169.47 | H-Bond (Protein Donor) |
| C1' | CB | SER- 46 | 3.47 | 0 | Hydrophobic |
| N | OD2 | ASP- 66 | 3.35 | 135.96 | H-Bond (Ligand Donor) |
| N | OD2 | ASP- 66 | 3.35 | 0 | Ionic (Ligand Cationic) |
| NE2 | OH | TYR- 211 | 2.67 | 162.07 | H-Bond (Ligand Donor) |
| CG | CE1 | TYR- 211 | 3.61 | 0 | Hydrophobic |
| CG | CB | CYS- 229 | 4.45 | 0 | Hydrophobic |
| C2' | CG2 | THR- 230 | 4.1 | 0 | Hydrophobic |
| CG | CZ | PHE- 233 | 3.61 | 0 | Hydrophobic |
| N1 | N | LEU- 261 | 2.79 | 151.89 | H-Bond (Protein Donor) |
| N6 | O | LEU- 261 | 3.11 | 166.74 | H-Bond (Ligand Donor) |
| O2S | NZ | LYS- 270 | 2.89 | 144.24 | H-Bond (Protein Donor) |
