sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
1999-11-05
| Name: | Phospholipase A2, membrane associated |
|---|---|
| ID: | PA2GA_HUMAN |
| AC: | P14555 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 22.718 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | CA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.489 | 502.875 |
| % Hydrophobic | % Polar |
|---|---|
| 53.02 | 46.98 |
| According to VolSite | |
| HET Code: | I3N |
|---|---|
| Formula: | C19H18NO3 |
| Molecular weight: | 308.351 g/mol |
| DrugBank ID: | DB03121 |
| Buried Surface Area: | 66.96 % |
| Polar Surface area: | 54.29 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 59.748 | 30.8797 | 46.5274 |
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 | 4.03 | 0 | Hydrophobic |
| C20 | CB | LEU- 2 | 4.43 | 0 | Hydrophobic |
| C12 | CE2 | PHE- 5 | 3.95 | 0 | Hydrophobic |
| C16 | CE2 | PHE- 5 | 4.18 | 0 | Hydrophobic |
| C20 | CB | PHE- 5 | 4.33 | 0 | Hydrophobic |
| C21 | CB | HIS- 6 | 3.52 | 0 | Hydrophobic |
| C19 | CB | ALA- 17 | 4.05 | 0 | Hydrophobic |
| C23 | CB | ALA- 18 | 4.24 | 0 | Hydrophobic |
| C16 | CB | TYR- 21 | 3.88 | 0 | Hydrophobic |
| C16 | CB | CYS- 28 | 4.5 | 0 | Hydrophobic |
| O14 | N | GLY- 29 | 3.11 | 130.54 | H-Bond (Protein Donor) |
| C8 | CG2 | VAL- 30 | 3.88 | 0 | Hydrophobic |
| C12 | SG | CYS- 44 | 3.98 | 0 | Hydrophobic |
| C16 | SG | CYS- 44 | 4.37 | 0 | Hydrophobic |
| C12 | CB | HIS- 47 | 4.49 | 0 | Hydrophobic |
| C1 | CD2 | TYR- 51 | 3.65 | 0 | Hydrophobic |
| C16 | CZ | PHE- 98 | 4.05 | 0 | Hydrophobic |
| O14 | CA | CA- 198 | 2.63 | 0 | Metal Acceptor |
