sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.400 Å
X-ray
2010-06-18
| Name: | Acidic phospholipase A2 3 |
|---|---|
| ID: | PA2A3_NAJSG |
| AC: | P60045 |
| Organism: | Naja sagittifera |
| Reign: | Eukaryota |
| TaxID: | 195058 |
| EC Number: | 3.1.1.4 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 22.319 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | CA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.860 | 324.000 |
| % Hydrophobic | % Polar |
|---|---|
| 54.17 | 45.83 |
| According to VolSite | |
| HET Code: | ANN |
|---|---|
| Formula: | C8H7O3 |
| Molecular weight: | 151.139 g/mol |
| DrugBank ID: | DB02795 |
| Buried Surface Area: | 61 % |
| Polar Surface area: | 49.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -5.86982 | -10.2256 | -2.05964 |
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 |
| C8 | CD1 | LEU- 2 | 4 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 2 | 3.49 | 0 | Hydrophobic |
| C8 | CD2 | PHE- 5 | 4.04 | 0 | Hydrophobic |
| C8 | CB | LYS- 6 | 4.32 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 9 | 3.84 | 0 | Hydrophobic |
| C8 | CZ3 | TRP- 19 | 3.86 | 0 | Hydrophobic |
| O2 | N | GLY- 30 | 3 | 155.64 | H-Bond (Protein Donor) |
| O2 | CA | CA- 122 | 2.54 | 0 | Metal Acceptor |
