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
1996-02-13
| Name: | Parathion hydrolase |
|---|---|
| ID: | OPD_BREDI |
| AC: | P0A434 |
| Organism: | Brevundimonas diminuta |
| Reign: | Bacteria |
| TaxID: | 293 |
| EC Number: | 3.1.8.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 21.941 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.844 | 675.000 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | EBP |
|---|---|
| Formula: | C12H19O3P |
| Molecular weight: | 242.251 g/mol |
| DrugBank ID: | DB02138 |
| Buried Surface Area: | 65.04 % |
| Polar Surface area: | 45.34 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 47.5182 | -8.40937 | 31.5104 |
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 |
| C12 | CG2 | ILE- 106 | 4.41 | 0 | Hydrophobic |
| O3 | NE1 | TRP- 131 | 3.28 | 131.48 | H-Bond (Protein Donor) |
| C9 | CZ2 | TRP- 131 | 3.82 | 0 | Hydrophobic |
| C11 | CZ2 | TRP- 131 | 3.92 | 0 | Hydrophobic |
| C9 | CZ | PHE- 132 | 4.06 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 271 | 4.21 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 271 | 3.28 | 0 | Hydrophobic |
| C3 | CB | ASP- 301 | 4.5 | 0 | Hydrophobic |
| C8 | CZ3 | TRP- 302 | 4.25 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 303 | 4.04 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 303 | 4.46 | 0 | Hydrophobic |
| C10 | CZ | PHE- 306 | 4.28 | 0 | Hydrophobic |
| C10 | CD1 | TYR- 309 | 4.19 | 0 | Hydrophobic |
| C4 | SD | MET- 317 | 4.07 | 0 | Hydrophobic |
| C8 | CE | MET- 317 | 3.26 | 0 | Hydrophobic |
