sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.100 Å
X-ray
2005-07-29
| Name: | Beta-elicitin cinnamomin |
|---|---|
| ID: | ELIB_PHYCI |
| AC: | P15569 |
| Organism: | Phytophthora cinnamomi |
| Reign: | Eukaryota |
| TaxID: | 4785 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 5 % |
| B | 95 % |
| B-Factor: | 13.662 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 2.198 | 661.500 |
| % Hydrophobic | % Polar |
|---|---|
| 78.57 | 21.43 |
| According to VolSite | |
| HET Code: | ERG |
|---|---|
| Formula: | C28H44O |
| Molecular weight: | 396.648 g/mol |
| DrugBank ID: | DB04038 |
| Buried Surface Area: | 69.15 % |
| Polar Surface area: | 20.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 24.5101 | 16.0162 | 45.1326 |
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 |
| C27 | CD1 | TYR- 12 | 4.2 | 0 | Hydrophobic |
| C21 | CB | LEU- 15 | 4.15 | 0 | Hydrophobic |
| C27 | CB | LEU- 15 | 3.61 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 16 | 3.38 | 0 | Hydrophobic |
| C27 | CB | VAL- 16 | 4.48 | 0 | Hydrophobic |
| C18 | CE1 | PHE- 24 | 4.03 | 0 | Hydrophobic |
| C15 | CB | MET- 35 | 4.12 | 0 | Hydrophobic |
| C18 | SD | MET- 35 | 3.91 | 0 | Hydrophobic |
| C28 | CD2 | LEU- 36 | 3.75 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 41 | 4.41 | 0 | Hydrophobic |
| C4 | CG | PRO- 42 | 3.92 | 0 | Hydrophobic |
| C3 | CE2 | TYR- 47 | 4.36 | 0 | Hydrophobic |
| C4 | CZ | TYR- 47 | 4.37 | 0 | Hydrophobic |
| O1 | OH | TYR- 47 | 2.65 | 163.03 | H-Bond (Protein Donor) |
| C19 | CE | MET- 50 | 4.01 | 0 | Hydrophobic |
| C19 | CE | MET- 59 | 3.91 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 60 | 4.02 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 60 | 3.79 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 63 | 4.13 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 63 | 3.74 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 75 | 4.11 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 75 | 3.84 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 75 | 4.48 | 0 | Hydrophobic |
| C28 | CG1 | VAL- 75 | 4.17 | 0 | Hydrophobic |
| C26 | CG | PRO- 76 | 4.06 | 0 | Hydrophobic |
| C28 | CG | PRO- 76 | 3.95 | 0 | Hydrophobic |
| C28 | CG2 | THR- 77 | 3.85 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 82 | 4 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 82 | 4.44 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 84 | 3.81 | 0 | Hydrophobic |
| C3 | CB | TYR- 87 | 3.8 | 0 | Hydrophobic |
| C2 | CD1 | PHE- 91 | 4.34 | 0 | Hydrophobic |
