sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.210 Å
X-ray
2007-07-03
| Name: | Basic phospholipase A2 VRV-PL-VIIIa |
|---|---|
| ID: | PA2B8_DABRR |
| AC: | P59071 |
| Organism: | Daboia russelii |
| Reign: | Eukaryota |
| TaxID: | 31159 |
| EC Number: | 3.1.1.4 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 30.581 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 18 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.464 | 273.375 |
| % Hydrophobic | % Polar |
|---|---|
| 58.02 | 41.98 |
| According to VolSite | |
| HET Code: | PZZ |
|---|---|
| Formula: | C14H21N2O |
| Molecular weight: | 233.329 g/mol |
| DrugBank ID: | DB08447 |
| Buried Surface Area: | 34.25 % |
| Polar Surface area: | 40.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 21.7402 | 6.13429 | 8.71982 |
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 |
| C4 | CD2 | LEU- 2 | 4.37 | 0 | Hydrophobic |
| C8 | CG | LEU- 2 | 4.3 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 2 | 4.32 | 0 | Hydrophobic |
| C15 | CE2 | PHE- 5 | 4.16 | 0 | Hydrophobic |
| C16 | CB | CYS- 29 | 4.14 | 0 | Hydrophobic |
| C16 | SG | CYS- 45 | 4.48 | 0 | Hydrophobic |
| C4 | CD | LYS- 69 | 4.23 | 0 | Hydrophobic |
| O17 | O | HOH- 216 | 3.44 | 143.83 | H-Bond (Ligand Donor) |
