sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.010 Å
X-ray
2012-04-17
| Name: | Jasmonic acid-amido synthetase JAR1 |
|---|---|
| ID: | JAR1_ARATH |
| AC: | Q9SKE2 |
| Organism: | Arabidopsis thaliana |
| Reign: | Eukaryota |
| TaxID: | 3702 |
| EC Number: | 6.3.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 27.199 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.456 | 904.500 |
| % Hydrophobic | % Polar |
|---|---|
| 54.48 | 45.52 |
| According to VolSite | |
| HET Code: | JAI |
|---|---|
| Formula: | C18H28NO4 |
| Molecular weight: | 322.419 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.87 % |
| Polar Surface area: | 86.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 38.0445 | -19.7798 | -18.3921 |
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 |
| O1 | N | SER- 101 | 3.01 | 158.77 | H-Bond (Protein Donor) |
| O2 | OG | SER- 101 | 2.65 | 165.93 | H-Bond (Protein Donor) |
| CG2 | CB | SER- 101 | 4.35 | 0 | Hydrophobic |
| C01 | CE1 | PHE- 113 | 4.22 | 0 | Hydrophobic |
| C01 | CD1 | LEU- 117 | 3.87 | 0 | Hydrophobic |
| CG2 | CG2 | THR- 164 | 3.96 | 0 | Hydrophobic |
| CD1 | CB | THR- 164 | 3.44 | 0 | Hydrophobic |
| C02 | CB | ALA- 165 | 4.24 | 0 | Hydrophobic |
| C05 | CB | ALA- 165 | 4.14 | 0 | Hydrophobic |
| C06 | CG2 | THR- 166 | 4.05 | 0 | Hydrophobic |
| C12 | CG2 | THR- 166 | 4.47 | 0 | Hydrophobic |
| CD1 | CG2 | THR- 166 | 3.82 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 222 | 4.23 | 0 | Hydrophobic |
| C09 | CG1 | VAL- 222 | 3.98 | 0 | Hydrophobic |
| C12 | CZ | PHE- 223 | 3.45 | 0 | Hydrophobic |
| CG1 | CE2 | PHE- 223 | 4.49 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 304 | 3.69 | 0 | Hydrophobic |
| C02 | CE2 | TRP- 336 | 4.3 | 0 | Hydrophobic |
| C05 | CZ2 | TRP- 336 | 3.92 | 0 | Hydrophobic |
| C06 | CH2 | TRP- 336 | 4.39 | 0 | Hydrophobic |
| C09 | CH2 | TRP- 336 | 3.74 | 0 | Hydrophobic |
| O1 | O | HOH- 1038 | 3.19 | 122.23 | H-Bond (Protein Donor) |
