sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2012-09-24
| 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 | 95 % |
| B | 5 % |
| B-Factor: | 24.119 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 18 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | FE MN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.115 | 1289.250 |
| % Hydrophobic | % Polar |
|---|---|
| 46.86 | 53.14 |
| According to VolSite | |
| HET Code: | HL4 |
|---|---|
| Formula: | C8H13NO3 |
| Molecular weight: | 171.194 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.54 % |
| 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 |
|---|---|---|
| 2.3995 | 15.1338 | -11.2334 |
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 | 4.46 | 0 | Hydrophobic |
| O9 | OH | TYR- 30 | 2.9 | 135.31 | H-Bond (Protein Donor) |
| C11 | CE1 | PHE- 111 | 4.43 | 0 | Hydrophobic |
| C13 | CZ | PHE- 111 | 4.18 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 268 | 3.42 | 0 | Hydrophobic |
| C5 | CH2 | TRP- 271 | 3.62 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 278 | 3.8 | 0 | Hydrophobic |
| C10 | CE | MET- 286 | 3.88 | 0 | Hydrophobic |
| C4 | CZ2 | TRP- 289 | 4.39 | 0 | Hydrophobic |
| C5 | CH2 | TRP- 289 | 3.45 | 0 | Hydrophobic |
| C10 | CZ3 | TRP- 289 | 4.14 | 0 | Hydrophobic |
| C13 | CZ3 | TRP- 289 | 4.23 | 0 | Hydrophobic |
