sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2008-09-10
| Name: | Gibberellin receptor GID1A |
|---|---|
| ID: | GID1A_ARATH |
| AC: | Q9MAA7 |
| Organism: | Arabidopsis thaliana |
| Reign: | Eukaryota |
| TaxID: | 3702 |
| EC Number: | 3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 10.111 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.651 | 317.250 |
| % Hydrophobic | % Polar |
|---|---|
| 44.68 | 55.32 |
| According to VolSite | |
| HET Code: | GA4 |
|---|---|
| Formula: | C19H23O5 |
| Molecular weight: | 331.383 g/mol |
| DrugBank ID: | DB07815 |
| Buried Surface Area: | 75.46 % |
| Polar Surface area: | 86.66 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -10.0359 | 18.2347 | -5.05596 |
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 |
| C11 | CG2 | ILE- 24 | 3.86 | 0 | Hydrophobic |
| C1 | CD2 | PHE- 27 | 3.54 | 0 | Hydrophobic |
| C11 | CB | PHE- 27 | 4.27 | 0 | Hydrophobic |
| C12 | CB | LYS- 28 | 4.14 | 0 | Hydrophobic |
| C15 | CD2 | TYR- 31 | 3.95 | 0 | Hydrophobic |
| C9 | CE2 | TYR- 31 | 3.99 | 0 | Hydrophobic |
| O71 | OG | SER- 116 | 2.71 | 160.31 | H-Bond (Protein Donor) |
| C2 | CD1 | ILE- 126 | 3.91 | 0 | Hydrophobic |
| O31 | OH | TYR- 127 | 2.75 | 173.42 | H-Bond (Ligand Donor) |
| O72 | OG | SER- 191 | 3.17 | 143.83 | H-Bond (Protein Donor) |
| C18 | CB | SER- 191 | 3.96 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 239 | 3.58 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 323 | 4.17 | 0 | Hydrophobic |
