sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2001-04-02
| Name: | 12-oxophytodienoate reductase 1 |
|---|---|
| ID: | OPR1_SOLLC |
| AC: | Q9XG54 |
| Organism: | Solanum lycopersicum |
| Reign: | Eukaryota |
| TaxID: | 4081 |
| EC Number: | 1.3.1.42 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 34.203 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.335 | 1049.625 |
| % Hydrophobic | % Polar |
|---|---|
| 50.16 | 49.84 |
| According to VolSite | |
| HET Code: | OPD |
|---|---|
| Formula: | C18H27O3 |
| Molecular weight: | 291.405 g/mol |
| DrugBank ID: | DB03007 |
| Buried Surface Area: | 67.45 % |
| Polar Surface area: | 57.2 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| -4.11083 | 1.31778 | 10.056 |
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 | CB | THR- 37 | 4.39 | 0 | Hydrophobic |
| C11 | CZ | TYR- 78 | 4.45 | 0 | Hydrophobic |
| C16 | CD1 | TYR- 78 | 3.93 | 0 | Hydrophobic |
| C15 | CE1 | TYR- 78 | 3.56 | 0 | Hydrophobic |
| C17 | CE | MET- 142 | 3.49 | 0 | Hydrophobic |
| O20 | OG | SER- 143 | 3.34 | 137.11 | H-Bond (Protein Donor) |
| O20 | N | SER- 143 | 2.53 | 173.64 | H-Bond (Protein Donor) |
| O19 | OG | SER- 143 | 2.62 | 152.89 | H-Bond (Protein Donor) |
| O19 | N | SER- 143 | 3.47 | 127.39 | H-Bond (Protein Donor) |
| O6 | NE2 | HIS- 187 | 2.89 | 160.4 | H-Bond (Protein Donor) |
| O6 | ND1 | HIS- 190 | 2.98 | 172.5 | H-Bond (Protein Donor) |
| C6 | CB | HIS- 190 | 4.14 | 0 | Hydrophobic |
| C6 | CE2 | TYR- 192 | 4.12 | 0 | Hydrophobic |
| C11 | CE2 | TYR- 246 | 4.45 | 0 | Hydrophobic |
| C6 | CE2 | TYR- 246 | 3.51 | 0 | Hydrophobic |
| C12 | CZ | TYR- 358 | 3.59 | 0 | Hydrophobic |
| C14 | CE1 | TYR- 358 | 3.43 | 0 | Hydrophobic |
| C7 | C1' | FMN- 501 | 4.44 | 0 | Hydrophobic |
| C5 | C9A | FMN- 501 | 4.24 | 0 | Hydrophobic |
