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
2014-11-06
| 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 | 83 % |
| B | 17 % |
| B-Factor: | 22.486 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.142 | 432.000 |
| % Hydrophobic | % Polar |
|---|---|
| 53.91 | 46.09 |
| According to VolSite | |
| HET Code: | A3T |
|---|---|
| Formula: | C14H22N7O5 |
| Molecular weight: | 368.368 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 77.23 % |
| 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 |
|---|---|---|
| -9.39188 | 6.1585 | 15.9084 |
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 | 3.53 | 0 | Hydrophobic |
| C4' | CG | LEU- 20 | 4.4 | 0 | Hydrophobic |
| C5' | CD2 | LEU- 20 | 4.15 | 0 | Hydrophobic |
| N1 | N | VAL- 45 | 3.01 | 162.99 | H-Bond (Protein Donor) |
| N6 | O | VAL- 45 | 2.82 | 167.07 | H-Bond (Ligand Donor) |
| N | O | PRO- 80 | 3.32 | 173.95 | H-Bond (Ligand Donor) |
| C2' | CB | PRO- 80 | 3.74 | 0 | Hydrophobic |
| O | N | ALA- 82 | 2.89 | 145.09 | H-Bond (Protein Donor) |
| N6 | O | ALA- 89 | 3.4 | 143.83 | H-Bond (Ligand Donor) |
| C1' | CE1 | PHE- 117 | 3.4 | 0 | Hydrophobic |
| C2' | CD1 | PHE- 117 | 4.24 | 0 | Hydrophobic |
| O2' | N | GLY- 118 | 2.81 | 167.66 | H-Bond (Protein Donor) |
| N8 | O | TYR- 119 | 3.03 | 159.06 | H-Bond (Ligand Donor) |
| CG2 | CD1 | TYR- 120 | 3.5 | 0 | Hydrophobic |
| OG | N | MET- 121 | 3.19 | 167.94 | H-Bond (Protein Donor) |
| N | OE2 | GLU- 134 | 3.92 | 0 | Ionic (Ligand Cationic) |
| N | OE1 | GLU- 134 | 3.16 | 0 | Ionic (Ligand Cationic) |
| N | OE1 | GLU- 134 | 3.16 | 168.5 | H-Bond (Ligand Donor) |
| N | O | HOH- 5003 | 2.81 | 139.61 | H-Bond (Ligand Donor) |
| O | O | HOH- 5016 | 2.71 | 166.68 | H-Bond (Protein Donor) |
