sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.860 Å
X-ray
2010-10-22
| 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 | 18 % |
| B | 82 % |
| B-Factor: | 26.662 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.080 | 378.000 |
| % Hydrophobic | % Polar |
|---|---|
| 61.61 | 38.39 |
| According to VolSite | |
| HET Code: | A3T |
|---|---|
| Formula: | C14H22N7O5 |
| Molecular weight: | 368.368 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.71 % |
| 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 |
|---|---|---|
| 23.5182 | -3.92569 | 4.5375 |
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 | 3.38 | 0 | Hydrophobic |
| C1' | CD1 | LEU- 20 | 4.37 | 0 | Hydrophobic |
| C5' | CG | LEU- 20 | 3.95 | 0 | Hydrophobic |
| N1 | N | VAL- 45 | 3 | 169.55 | H-Bond (Protein Donor) |
| N6 | O | VAL- 45 | 2.79 | 161.4 | H-Bond (Ligand Donor) |
| C2' | CB | PRO- 80 | 3.93 | 0 | Hydrophobic |
| O | N | ALA- 82 | 2.93 | 147.33 | H-Bond (Protein Donor) |
| C1' | CE1 | PHE- 117 | 3.38 | 0 | Hydrophobic |
| C2' | CD1 | PHE- 117 | 4.36 | 0 | Hydrophobic |
| O2' | N | GLY- 118 | 2.84 | 162.99 | H-Bond (Protein Donor) |
| N8 | O | TYR- 119 | 2.94 | 159.59 | H-Bond (Ligand Donor) |
| CG2 | CD1 | TYR- 120 | 3.54 | 0 | Hydrophobic |
| OG | N | LYS- 121 | 3.19 | 170.22 | H-Bond (Protein Donor) |
| N | OE1 | GLU- 134 | 3.11 | 163.87 | H-Bond (Ligand Donor) |
| N | OE1 | GLU- 134 | 3.11 | 0 | Ionic (Ligand Cationic) |
| O | O | HOH- 1024 | 2.79 | 179.96 | H-Bond (Protein Donor) |
