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
2006-07-06
| Name: | Threonine--tRNA ligase |
|---|---|
| ID: | SYT_PYRAB |
| AC: | Q9UZ14 |
| Organism: | Pyrococcus abyssi |
| Reign: | Archaea |
| TaxID: | 272844 |
| EC Number: | 6.1.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 7 % |
| B | 93 % |
| B-Factor: | 41.362 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.826 | 408.375 |
| % Hydrophobic | % Polar |
|---|---|
| 57.02 | 42.98 |
| According to VolSite | |
| HET Code: | SSA |
|---|---|
| Formula: | C13H19N7O8S |
| Molecular weight: | 433.397 g/mol |
| DrugBank ID: | DB03869 |
| Buried Surface Area: | 53.18 % |
| Polar Surface area: | 250.09 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: | 7 |
| X | Y | Z |
|---|---|---|
| 9.52569 | -7.63062 | 15.6044 |
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 |
| N10 | O | ALA- 19 | 3.01 | 140.92 | H-Bond (Ligand Donor) |
| C5' | CB | ALA- 19 | 3.7 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 20 | 3.53 | 0 | Hydrophobic |
| N6 | O | VAL- 45 | 2.9 | 160.73 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 45 | 3.3 | 150.43 | H-Bond (Protein Donor) |
| C2' | CB | PRO- 80 | 4.4 | 0 | Hydrophobic |
| C5' | CB | ALA- 82 | 4.49 | 0 | Hydrophobic |
| C3' | CB | ALA- 82 | 3.46 | 0 | Hydrophobic |
| N6 | O | ALA- 89 | 3.48 | 147.33 | H-Bond (Ligand Donor) |
| C2' | CE1 | PHE- 117 | 4.44 | 0 | Hydrophobic |
| C1' | CZ | PHE- 117 | 3.39 | 0 | Hydrophobic |
| O2' | N | GLY- 118 | 3.08 | 149.14 | H-Bond (Protein Donor) |
| OG | OH | TYR- 120 | 2.98 | 135.75 | H-Bond (Ligand Donor) |
