sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2005-09-12
| Name: | Phospholipase A2, major isoenzyme |
|---|---|
| ID: | PA21B_PIG |
| AC: | P00592 |
| Organism: | Sus scrofa |
| Reign: | Eukaryota |
| TaxID: | 9823 |
| EC Number: | 3.1.1.4 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 23.990 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.289 | 732.375 |
| % Hydrophobic | % Polar |
|---|---|
| 55.76 | 44.24 |
| According to VolSite | |
| HET Code: | CHD |
|---|---|
| Formula: | C24H39O5 |
| Molecular weight: | 407.563 g/mol |
| DrugBank ID: | DB02659 |
| Buried Surface Area: | 60.26 % |
| Polar Surface area: | 100.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 37.5945 | 14.8868 | 16.5527 |
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 |
| C2 | CD1 | LEU- 2 | 4.37 | 0 | Hydrophobic |
| C1 | CE2 | PHE- 5 | 4.27 | 0 | Hydrophobic |
| C2 | CG | ARG- 6 | 4 | 0 | Hydrophobic |
| C21 | CG2 | ILE- 9 | 3.88 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 9 | 3.52 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 13 | 3.52 | 0 | Hydrophobic |
| C23 | CB | SER- 16 | 4.31 | 0 | Hydrophobic |
| C16 | CG | MET- 20 | 4.06 | 0 | Hydrophobic |
| O7 | O | ASN- 23 | 2.72 | 138.53 | H-Bond (Ligand Donor) |
| C15 | CB | TYR- 25 | 3.6 | 0 | Hydrophobic |
| C16 | CD2 | TYR- 25 | 4.42 | 0 | Hydrophobic |
| C8 | CB | CYS- 29 | 4.23 | 0 | Hydrophobic |
| C18 | SG | CYS- 29 | 4.29 | 0 | Hydrophobic |
| C19 | CB | CYS- 29 | 4.49 | 0 | Hydrophobic |
| C6 | CB | CYS- 29 | 4.31 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 41 | 3.88 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 41 | 3.86 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 41 | 4.35 | 0 | Hydrophobic |
| C18 | SG | CYS- 45 | 4.27 | 0 | Hydrophobic |
| C19 | SG | CYS- 45 | 4.48 | 0 | Hydrophobic |
| C18 | CZ | PHE- 106 | 3.84 | 0 | Hydrophobic |
| C21 | CB | PHE- 106 | 3.9 | 0 | Hydrophobic |
| C11 | CE2 | PHE- 106 | 3.79 | 0 | Hydrophobic |
| C16 | CD2 | TYR- 111 | 4.02 | 0 | Hydrophobic |
| C22 | CD2 | TYR- 111 | 4.26 | 0 | Hydrophobic |
