sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.200 Å
X-ray
2006-01-06
| 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 |
|---|---|
| D | 100 % |
| B-Factor: | 19.657 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.279 | 648.000 |
| % Hydrophobic | % Polar |
|---|---|
| 54.17 | 45.83 |
| According to VolSite | |
| HET Code: | ZEA |
|---|---|
| Formula: | C10H13N5O |
| Molecular weight: | 219.243 g/mol |
| DrugBank ID: | DB11337 |
| Buried Surface Area: | 62.34 % |
| Polar Surface area: | 86.72 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 56.2416 | 62.739 | 1.25806 |
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 |
| C15 | CD1 | LEU- 34 | 3.67 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 38 | 4.18 | 0 | Hydrophobic |
| C14 | CG | PHE- 56 | 3.3 | 0 | Hydrophobic |
| C14 | CE1 | PHE- 58 | 4.46 | 0 | Hydrophobic |
| O16 | NE2 | GLN- 67 | 2.95 | 148.34 | H-Bond (Protein Donor) |
| N1 | NE2 | GLN- 67 | 3.28 | 122.63 | H-Bond (Protein Donor) |
| C11 | CB | SER- 138 | 4.47 | 0 | Hydrophobic |
