sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
1999-11-02
| 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: | 24.801 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | CA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.454 | 465.750 |
| % Hydrophobic | % Polar |
|---|---|
| 53.62 | 46.38 |
| According to VolSite | |
| HET Code: | 6IN |
|---|---|
| Formula: | C22H23N2O4 |
| Molecular weight: | 379.429 g/mol |
| DrugBank ID: | DB02936 |
| Buried Surface Area: | 64.33 % |
| Polar Surface area: | 97.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 58.7765 | 29.778 | 46.6627 |
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 |
| C3 | CG | LEU- 2 | 4.37 | 0 | Hydrophobic |
| C18 | CB | LEU- 2 | 4.5 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 2 | 4.01 | 0 | Hydrophobic |
| C27 | CE2 | PHE- 5 | 4.47 | 0 | Hydrophobic |
| C32 | CE2 | PHE- 5 | 4.12 | 0 | Hydrophobic |
| C19 | CB | HIS- 6 | 4.01 | 0 | Hydrophobic |
| C18 | CB | ALA- 17 | 4.15 | 0 | Hydrophobic |
| C20 | CB | ALA- 18 | 4.18 | 0 | Hydrophobic |
| C27 | CB | TYR- 21 | 3.78 | 0 | Hydrophobic |
| C27 | CB | CYS- 28 | 4.28 | 0 | Hydrophobic |
| O40 | N | GLY- 29 | 3.01 | 134.16 | H-Bond (Protein Donor) |
| C2 | CG2 | VAL- 30 | 3.85 | 0 | Hydrophobic |
| O54 | N | GLY- 31 | 2.51 | 146.19 | H-Bond (Protein Donor) |
| C27 | SG | CYS- 44 | 4.31 | 0 | Hydrophobic |
| C32 | SG | CYS- 44 | 3.81 | 0 | Hydrophobic |
| N37 | ND1 | HIS- 47 | 3.05 | 153.95 | H-Bond (Ligand Donor) |
| N37 | OD2 | ASP- 48 | 2.86 | 146.86 | H-Bond (Ligand Donor) |
| C42 | CD2 | TYR- 51 | 3.51 | 0 | Hydrophobic |
| O52 | NZ | LYS- 52 | 3.67 | 0 | Ionic (Protein Cationic) |
| C27 | CZ | PHE- 98 | 4.28 | 0 | Hydrophobic |
| O40 | CA | CA- 198 | 2.56 | 0 | Metal Acceptor |
| O54 | CA | CA- 198 | 2.56 | 0 | Metal Acceptor |
