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
2013-08-15
| Name: | Ara h 8 allergen |
|---|---|
| ID: | Q6VT83_ARAHY |
| AC: | Q6VT83 |
| Organism: | Arachis hypogaea |
| Reign: | Eukaryota |
| TaxID: | 3818 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 91 % |
| B | 9 % |
| B-Factor: | 31.925 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.176 | 789.750 |
| % Hydrophobic | % Polar |
|---|---|
| 59.83 | 40.17 |
| According to VolSite | |
| HET Code: | 28E |
|---|---|
| Formula: | C15H14O6 |
| Molecular weight: | 290.268 g/mol |
| DrugBank ID: | DB12039 |
| Buried Surface Area: | 63.35 % |
| Polar Surface area: | 110.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 10.6941 | -0.389762 | 16.0473 |
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 |
| CAU | CG2 | THR- 30 | 3.85 | 0 | Hydrophobic |
| CAI | CB | THR- 30 | 3.64 | 0 | Hydrophobic |
| OAC | OG1 | THR- 30 | 2.85 | 148.07 | H-Bond (Ligand Donor) |
| CAP | CD1 | ILE- 34 | 4.24 | 0 | Hydrophobic |
| CAY | CG2 | ILE- 34 | 4.1 | 0 | Hydrophobic |
| CAI | CG1 | VAL- 37 | 4.43 | 0 | Hydrophobic |
| CAJ | CG2 | VAL- 37 | 4.19 | 0 | Hydrophobic |
| CAK | CG2 | VAL- 37 | 4.07 | 0 | Hydrophobic |
| CAJ | CD2 | LEU- 55 | 3.47 | 0 | Hydrophobic |
| CAT | CG2 | ILE- 57 | 4.1 | 0 | Hydrophobic |
| CAN | CD1 | ILE- 66 | 3.8 | 0 | Hydrophobic |
| OAQ | OH | TYR- 82 | 3.08 | 141.45 | H-Bond (Ligand Donor) |
| DuAr | NZ | LYS- 138 | 3.63 | 31.34 | Pi/Cation |
| CBD | CG | LYS- 138 | 3.92 | 0 | Hydrophobic |
| CBE | CB | LEU- 142 | 4.28 | 0 | Hydrophobic |
| CAV | CD1 | LEU- 142 | 3.54 | 0 | Hydrophobic |
