sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2010-07-19
| Name: | Glutamate--tRNA ligase 2 |
|---|---|
| ID: | SYE2_THEMA |
| AC: | Q9X2I8 |
| Organism: | Thermotoga maritima |
| Reign: | Bacteria |
| TaxID: | 243274 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 30.233 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.878 | 671.625 |
| % Hydrophobic | % Polar |
|---|---|
| 38.19 | 61.81 |
| According to VolSite | |
| HET Code: | GSU |
|---|---|
| Formula: | C15H20N7O9S |
| Molecular weight: | 474.426 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.12 % |
| Polar Surface area: | 269.99 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 13 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -2.58275 | 61.8818 | 3.54906 |
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 |
| OE1 | CZ | ARG- 28 | 3.88 | 0 | Ionic (Protein Cationic) |
| OE2 | CZ | ARG- 28 | 3.74 | 0 | Ionic (Protein Cationic) |
| OE1 | NH1 | ARG- 28 | 3.39 | 153.2 | H-Bond (Protein Donor) |
| OE1 | NH2 | ARG- 28 | 3.44 | 150.55 | H-Bond (Protein Donor) |
| OE2 | NH2 | ARG- 28 | 2.78 | 138.15 | H-Bond (Protein Donor) |
| C4' | CE1 | PHE- 29 | 3.69 | 0 | Hydrophobic |
| CB | CB | ALA- 30 | 4.38 | 0 | Hydrophobic |
| C5' | CB | PRO- 31 | 4.4 | 0 | Hydrophobic |
| O2S | N | SER- 32 | 2.93 | 168.54 | H-Bond (Protein Donor) |
| C4' | CG2 | THR- 44 | 4.38 | 0 | Hydrophobic |
| C1' | CG2 | THR- 44 | 3.97 | 0 | Hydrophobic |
| N | OE1 | GLU- 64 | 2.68 | 153.62 | H-Bond (Ligand Donor) |
| N | OE1 | GLU- 64 | 2.68 | 0 | Ionic (Ligand Cationic) |
| CB | CE2 | TYR- 198 | 3.67 | 0 | Hydrophobic |
| CG | CD | ARG- 216 | 4.19 | 0 | Hydrophobic |
| O2' | N | GLY- 217 | 2.84 | 124.25 | H-Bond (Protein Donor) |
| O3' | N | GLY- 217 | 3.49 | 147.82 | H-Bond (Protein Donor) |
| O2' | OD1 | ASP- 219 | 2.96 | 146.66 | H-Bond (Ligand Donor) |
| O | NE2 | HIS- 220 | 2.8 | 169.16 | H-Bond (Protein Donor) |
| N1 | N | ILE- 247 | 2.85 | 168.88 | H-Bond (Protein Donor) |
