sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2010-08-22
| Name: | Phosphotriesterase |
|---|---|
| ID: | Q5KZU5_GEOKA |
| AC: | Q5KZU5 |
| Organism: | Geobacillus kaustophilus |
| Reign: | Bacteria |
| TaxID: | 235909 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 22.815 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN FE |
| Ligandability | Volume (Å3) |
|---|---|
| 0.906 | 654.750 |
| % Hydrophobic | % Polar |
|---|---|
| 48.97 | 51.03 |
| According to VolSite | |
| HET Code: | HL4 |
|---|---|
| Formula: | C8H13NO3 |
| Molecular weight: | 171.194 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.22 % |
| Polar Surface area: | 55.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 5.33483 | -8.73242 | -18.1913 |
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 | CE1 | PHE- 28 | 3.66 | 0 | Hydrophobic |
| C5 | CZ | TYR- 30 | 4.5 | 0 | Hydrophobic |
| O9 | OH | TYR- 30 | 3.29 | 154.82 | H-Bond (Protein Donor) |
| C10 | CG2 | ILE- 233 | 4.44 | 0 | Hydrophobic |
| C10 | SD | MET- 236 | 4.27 | 0 | Hydrophobic |
| C11 | CE | MET- 236 | 3.37 | 0 | Hydrophobic |
| C13 | SD | MET- 236 | 4.01 | 0 | Hydrophobic |
| OAP | ND2 | ASN- 266 | 3.4 | 131.09 | H-Bond (Protein Donor) |
| C4 | CG2 | VAL- 268 | 3.52 | 0 | Hydrophobic |
| C13 | CZ2 | TRP- 271 | 3.92 | 0 | Hydrophobic |
| C5 | CH2 | TRP- 271 | 3.36 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 278 | 4.26 | 0 | Hydrophobic |
| C10 | CE | MET- 286 | 3.73 | 0 | Hydrophobic |
| C5 | CH2 | TRP- 289 | 4.09 | 0 | Hydrophobic |
| C13 | CZ3 | TRP- 289 | 3.92 | 0 | Hydrophobic |
