sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2007-10-09
| Name: | Phenylalanine--tRNA ligase alpha subunit |
|---|---|
| ID: | SYFA_STAHJ |
| AC: | Q4L5E3 |
| Organism: | Staphylococcus haemolyticus |
| Reign: | Bacteria |
| TaxID: | 279808 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 43.074 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.916 | 688.500 |
| % Hydrophobic | % Polar |
|---|---|
| 48.53 | 51.47 |
| According to VolSite | |
| HET Code: | GAX |
|---|---|
| Formula: | C19H20N6O3S2 |
| Molecular weight: | 444.530 g/mol |
| DrugBank ID: | DB07817 |
| Buried Surface Area: | 61.65 % |
| Polar Surface area: | 144.15 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 97.521 | -10.4308 | 17.3773 |
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 |
| S2 | CD2 | LEU- 146 | 4.32 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 148 | 4.4 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 148 | 4.24 | 0 | Hydrophobic |
| C17 | CB | ALA- 154 | 4.37 | 0 | Hydrophobic |
| N2 | OG | SER- 174 | 2.86 | 144.07 | H-Bond (Ligand Donor) |
| N3 | NE2 | GLN- 177 | 2.98 | 153.32 | H-Bond (Protein Donor) |
| O2 | NE2 | GLN- 214 | 3.08 | 125.83 | H-Bond (Protein Donor) |
| N2 | OE1 | GLU- 216 | 3.03 | 145.92 | H-Bond (Ligand Donor) |
| S2 | CD1 | LEU- 218 | 4.46 | 0 | Hydrophobic |
| C12 | CD1 | PHE- 254 | 3.3 | 0 | Hydrophobic |
| C11 | CE1 | PHE- 254 | 3.59 | 0 | Hydrophobic |
| C17 | CG | PRO- 255 | 4.32 | 0 | Hydrophobic |
| C13 | CZ | PHE- 256 | 3.81 | 0 | Hydrophobic |
| C12 | CZ | PHE- 256 | 4.26 | 0 | Hydrophobic |
| C1 | CG2 | THR- 257 | 3.73 | 0 | Hydrophobic |
| S2 | CG2 | VAL- 292 | 4.14 | 0 | Hydrophobic |
| S2 | CG1 | VAL- 296 | 4.2 | 0 | Hydrophobic |
| S2 | CB | ALA- 311 | 3.98 | 0 | Hydrophobic |
| C1 | CB | ALA- 311 | 4.46 | 0 | Hydrophobic |
