sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2014-11-06
| Name: | Threonine--tRNA ligase |
|---|---|
| ID: | SYT_METJA |
| AC: | Q58597 |
| Organism: | Methanocaldococcus jannaschii |
| Reign: | Archaea |
| TaxID: | 243232 |
| EC Number: | 6.1.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 8 % |
| D | 92 % |
| B-Factor: | 24.230 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.869 | 445.500 |
| % Hydrophobic | % Polar |
|---|---|
| 56.06 | 43.94 |
| According to VolSite | |
| HET Code: | A3S |
|---|---|
| Formula: | C13H20N7O5 |
| Molecular weight: | 354.342 g/mol |
| DrugBank ID: | DB04024 |
| Buried Surface Area: | 65.76 % |
| Polar Surface area: | 196.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 32.741 | 4.92588 | 17.1335 |
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 |
| C5' | CG2 | THR- 23 | 4.26 | 0 | Hydrophobic |
| C1' | CD1 | ILE- 25 | 4.48 | 0 | Hydrophobic |
| C5' | CD1 | ILE- 25 | 4.27 | 0 | Hydrophobic |
| N1 | N | VAL- 46 | 3.12 | 163.48 | H-Bond (Protein Donor) |
| N6 | O | VAL- 46 | 2.83 | 160.85 | H-Bond (Ligand Donor) |
| C2' | CB | PRO- 81 | 4.1 | 0 | Hydrophobic |
| C2' | CB | ALA- 83 | 4.5 | 0 | Hydrophobic |
| O | N | ALA- 83 | 2.81 | 157.68 | H-Bond (Protein Donor) |
| C1' | CE1 | PHE- 118 | 3.61 | 0 | Hydrophobic |
| O2' | N | GLY- 119 | 2.99 | 164.64 | H-Bond (Protein Donor) |
| N | OE2 | GLU- 135 | 3.65 | 0 | Ionic (Ligand Cationic) |
| CB | CB | GLU- 135 | 4.33 | 0 | Hydrophobic |
| N | O | HOH- 605 | 3.42 | 140.29 | H-Bond (Ligand Donor) |
