sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2005-01-24
| Name: | Tryptophan synthase alpha chain |
|---|---|
| ID: | TRPA_THET2 |
| AC: | P16608 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 262724 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.085 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.838 | 378.000 |
| % Hydrophobic | % Polar |
|---|---|
| 45.54 | 54.46 |
| According to VolSite | |
| HET Code: | IPL |
|---|---|
| Formula: | C11H12NO4P |
| Molecular weight: | 253.191 g/mol |
| DrugBank ID: | DB03171 |
| Buried Surface Area: | 58.12 % |
| Polar Surface area: | 98.02 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -4.72694 | 6.88271 | 13.1386 |
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 |
| C2' | CG | TYR- 21 | 3.72 | 0 | Hydrophobic |
| C3' | CD1 | TYR- 21 | 4.04 | 0 | Hydrophobic |
| C2' | CD1 | ILE- 62 | 4.05 | 0 | Hydrophobic |
| C8 | CE | MET- 97 | 4.03 | 0 | Hydrophobic |
| C6 | CB | PRO- 126 | 4.35 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 150 | 3.71 | 0 | Hydrophobic |
| C3' | CZ | TYR- 172 | 4.36 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 174 | 4.15 | 0 | Hydrophobic |
| O3P | N | GLY- 210 | 3.05 | 158.89 | H-Bond (Protein Donor) |
| C1' | CG1 | VAL- 227 | 3.89 | 0 | Hydrophobic |
| O2P | N | GLY- 229 | 2.77 | 156.83 | H-Bond (Protein Donor) |
| O1P | N | SER- 230 | 3.48 | 148.24 | H-Bond (Protein Donor) |
| O1P | OG | SER- 230 | 2.69 | 148.8 | H-Bond (Protein Donor) |
| O2P | N | SER- 230 | 3.42 | 144.37 | H-Bond (Protein Donor) |
| O2P | O | HOH- 2014 | 2.8 | 179.97 | H-Bond (Protein Donor) |
