sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.420 Å
X-ray
2014-03-07
| Name: | Cytokinin-specific binding protein |
|---|---|
| ID: | Q9ZWP8_VIGRA |
| AC: | Q9ZWP8 |
| Organism: | Vigna radiata |
| Reign: | Eukaryota |
| TaxID: | 157791 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 18.708 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.136 | 556.875 |
| % Hydrophobic | % Polar |
|---|---|
| 53.33 | 46.67 |
| According to VolSite | |
| HET Code: | GA3 |
|---|---|
| Formula: | C19H21O6 |
| Molecular weight: | 345.366 g/mol |
| DrugBank ID: | DB07814 |
| Buried Surface Area: | 66.95 % |
| Polar Surface area: | 106.89 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 11.674 | 1.16904 | 19.8273 |
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 |
| C9 | CD1 | LEU- 34 | 4.08 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 37 | 4.05 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 38 | 4.1 | 0 | Hydrophobic |
| C10 | CE2 | PHE- 56 | 4.45 | 0 | Hydrophobic |
| C3 | CZ | PHE- 56 | 4.5 | 0 | Hydrophobic |
| C12 | CE1 | PHE- 58 | 4.1 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 83 | 3.77 | 0 | Hydrophobic |
| C18 | CB | THR- 100 | 3.93 | 0 | Hydrophobic |
| O71 | OG1 | THR- 139 | 3.44 | 130.09 | H-Bond (Protein Donor) |
| O72 | OG1 | THR- 139 | 2.73 | 172 | H-Bond (Protein Donor) |
| C5 | CD2 | TYR- 142 | 4.45 | 0 | Hydrophobic |
| C15 | CB | TYR- 142 | 4.49 | 0 | Hydrophobic |
| C3 | CE2 | TYR- 142 | 4.28 | 0 | Hydrophobic |
