sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.970 Å
X-ray
2014-11-06
| Name: | Probable threonine--tRNA ligase 2 |
|---|---|
| ID: | SYT2_AERPE |
| AC: | Q9YFY3 |
| Organism: | Aeropyrum pernix |
| Reign: | Archaea |
| TaxID: | 272557 |
| EC Number: | 6.1.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 32.405 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.855 | 347.625 |
| % Hydrophobic | % Polar |
|---|---|
| 57.28 | 42.72 |
| According to VolSite | |
| HET Code: | A3S |
|---|---|
| Formula: | C13H20N7O5 |
| Molecular weight: | 354.342 g/mol |
| DrugBank ID: | DB04024 |
| Buried Surface Area: | 71.68 % |
| 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 |
|---|---|---|
| -2.83408 | 14.3841 | 3.12272 |
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' | CB | ALA- 19 | 3.3 | 0 | Hydrophobic |
| N1 | N | VAL- 42 | 3 | 157.77 | H-Bond (Protein Donor) |
| N6 | O | VAL- 42 | 2.9 | 168.15 | H-Bond (Ligand Donor) |
| C2' | CB | PRO- 74 | 4.09 | 0 | Hydrophobic |
| O | N | ALA- 76 | 2.81 | 144.14 | H-Bond (Protein Donor) |
| N6 | O | ALA- 83 | 3.28 | 140.01 | H-Bond (Ligand Donor) |
| C1' | CE2 | PHE- 112 | 3.62 | 0 | Hydrophobic |
| O2' | N | GLY- 113 | 3.04 | 165.6 | H-Bond (Protein Donor) |
| N8 | O | TRP- 114 | 3.06 | 171.95 | H-Bond (Ligand Donor) |
| CB | CD1 | TYR- 115 | 4.23 | 0 | Hydrophobic |
| OG | N | LYS- 116 | 2.95 | 171.96 | H-Bond (Protein Donor) |
