sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 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 | 87 % |
| B | 13 % |
| B-Factor: | 23.503 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.940 | 425.250 |
| % Hydrophobic | % Polar |
|---|---|
| 57.94 | 42.06 |
| According to VolSite | |
| HET Code: | A3S |
|---|---|
| Formula: | C13H20N7O5 |
| Molecular weight: | 354.342 g/mol |
| DrugBank ID: | DB04024 |
| Buried Surface Area: | 71.25 % |
| 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 |
|---|---|---|
| 22.9581 | 5.21128 | -3.96448 |
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 |
| C4' | CB | ALA- 19 | 3.73 | 0 | Hydrophobic |
| N1 | N | VAL- 45 | 3.12 | 170.33 | H-Bond (Protein Donor) |
| N6 | O | VAL- 45 | 2.9 | 158.6 | H-Bond (Ligand Donor) |
| C2' | CB | PRO- 80 | 3.89 | 0 | Hydrophobic |
| N | O | PRO- 80 | 3.47 | 143.03 | H-Bond (Ligand Donor) |
| O | N | ALA- 82 | 2.81 | 150.64 | H-Bond (Protein Donor) |
| C1' | CE1 | PHE- 117 | 3.49 | 0 | Hydrophobic |
| C2' | CD1 | PHE- 117 | 4.24 | 0 | Hydrophobic |
| O2' | N | GLY- 118 | 2.83 | 164.71 | H-Bond (Protein Donor) |
| N8 | O | TYR- 119 | 3.16 | 173.13 | H-Bond (Ligand Donor) |
| CB | CD1 | TYR- 120 | 4.03 | 0 | Hydrophobic |
| OG | N | LYS- 121 | 3.22 | 168.85 | H-Bond (Protein Donor) |
| N | OE2 | GLU- 134 | 3.81 | 0 | Ionic (Ligand Cationic) |
| N | OE1 | GLU- 134 | 2.64 | 0 | Ionic (Ligand Cationic) |
| N | OE1 | GLU- 134 | 2.64 | 146.93 | H-Bond (Ligand Donor) |
| OG | OE2 | GLU- 134 | 3.27 | 126.19 | H-Bond (Ligand Donor) |
| O2' | O | HOH- 1224 | 2.97 | 179.97 | H-Bond (Protein Donor) |
