sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.540 Å
X-ray
2011-11-18
| Name: | Major pollen allergen Bet v 1-A |
|---|---|
| ID: | BEV1A_BETPN |
| AC: | P15494 |
| Organism: | Betula pendula |
| Reign: | Eukaryota |
| TaxID: | 3505 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 11.560 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.575 | 1113.750 |
| % Hydrophobic | % Polar |
|---|---|
| 64.55 | 35.45 |
| According to VolSite | |
| HET Code: | DXC |
|---|---|
| Formula: | C24H39O4 |
| Molecular weight: | 391.564 g/mol |
| DrugBank ID: | DB03619 |
| Buried Surface Area: | 63.22 % |
| Polar Surface area: | 80.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 11.1465 | -0.21275 | 12.6272 |
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 |
| C24 | CE1 | PHE- 22 | 3.62 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 23 | 4.41 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 23 | 4.12 | 0 | Hydrophobic |
| O4 | OD1 | ASP- 27 | 2.6 | 154.63 | H-Bond (Ligand Donor) |
| C20 | CE2 | PHE- 30 | 4.04 | 0 | Hydrophobic |
| C24 | CE2 | PHE- 30 | 3.54 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 38 | 4.07 | 0 | Hydrophobic |
| C15 | CG1 | ILE- 56 | 4.22 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 56 | 4.5 | 0 | Hydrophobic |
| C18 | CE1 | PHE- 58 | 3.95 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 67 | 3.75 | 0 | Hydrophobic |
| C15 | CB | ASP- 69 | 4.35 | 0 | Hydrophobic |
| C21 | CE2 | TYR- 81 | 3.43 | 0 | Hydrophobic |
| C11 | CE2 | TYR- 83 | 3.65 | 0 | Hydrophobic |
| C17 | CZ | TYR- 83 | 4.05 | 0 | Hydrophobic |
| C11 | CE2 | TYR- 83 | 3.65 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 85 | 4.38 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 85 | 4.04 | 0 | Hydrophobic |
| O2 | ND2 | ASN- 100 | 3.02 | 144.9 | H-Bond (Protein Donor) |
| O2 | OG | SER- 136 | 2.76 | 146.9 | H-Bond (Protein Donor) |
| C1 | CB | SER- 136 | 3.95 | 0 | Hydrophobic |
| C18 | CG | MET- 139 | 3.62 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 143 | 3.73 | 0 | Hydrophobic |
