sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2000-09-25
| 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 | 46 % |
| B | 54 % |
| B-Factor: | 29.982 |
|---|---|
| Number of residues: | 48 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | CA CA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.994 | 583.875 |
| % Hydrophobic | % Polar |
|---|---|
| 57.23 | 42.77 |
| According to VolSite | |
| HET Code: | MJI |
|---|---|
| Formula: | C22H43F3O6P |
| Molecular weight: | 491.542 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.57 % |
| Polar Surface area: | 86.86 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 0 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 24 |
| X | Y | Z |
|---|---|---|
| 40.4016 | 37.0197 | 32.2536 |
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 |
| C1 | CD1 | LEU- 2 | 4.41 | 0 | Hydrophobic |
| C31 | CD1 | LEU- 2 | 4.08 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 2 | 4.11 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 2 | 4.15 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 2 | 4.14 | 0 | Hydrophobic |
| C26 | CD1 | LEU- 2 | 3.38 | 0 | Hydrophobic |
| F31 | CZ | PHE- 5 | 3.41 | 0 | Hydrophobic |
| C2P | CE2 | PHE- 5 | 4.48 | 0 | Hydrophobic |
| C18 | CE2 | PHE- 5 | 4.07 | 0 | Hydrophobic |
| C32 | CE2 | PHE- 5 | 3.93 | 0 | Hydrophobic |
| C21 | CE2 | PHE- 5 | 3.7 | 0 | Hydrophobic |
| C26 | CD2 | PHE- 5 | 3.72 | 0 | Hydrophobic |
| C26 | CB | ARG- 6 | 3.49 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 9 | 3.64 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 9 | 3.44 | 0 | Hydrophobic |
| F31 | CD1 | ILE- 9 | 3.38 | 0 | Hydrophobic |
| F32 | CB | PRO- 18 | 3.98 | 0 | Hydrophobic |
| C25 | CB | PRO- 18 | 4.38 | 0 | Hydrophobic |
| C23 | CB | PRO- 18 | 3.88 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 19 | 4.32 | 0 | Hydrophobic |
| C31 | CD1 | LEU- 19 | 4.42 | 0 | Hydrophobic |
| F32 | CD1 | LEU- 19 | 4.07 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 19 | 3.38 | 0 | Hydrophobic |
| F33 | CB | PHE- 22 | 3.23 | 0 | Hydrophobic |
| C2P | CB | PHE- 22 | 4.4 | 0 | Hydrophobic |
| C20 | CB | PHE- 22 | 4.08 | 0 | Hydrophobic |
| C22 | CB | PHE- 22 | 3.7 | 0 | Hydrophobic |
| C3 | CB | ASN- 23 | 3.3 | 0 | Hydrophobic |
| C2P | CB | CYS- 29 | 4.13 | 0 | Hydrophobic |
| C19 | CB | CYS- 29 | 4.38 | 0 | Hydrophobic |
| O21 | N | GLY- 30 | 2.89 | 153.62 | H-Bond (Protein Donor) |
| C11 | CB | LEU- 31 | 4.34 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 31 | 3.3 | 0 | Hydrophobic |
| C2P | SG | CYS- 45 | 3.95 | 0 | Hydrophobic |
| C1 | CE2 | TYR- 69 | 4.49 | 0 | Hydrophobic |
| C15 | CE2 | TYR- 69 | 4.2 | 0 | Hydrophobic |
| C18 | CZ | TYR- 69 | 4.38 | 0 | Hydrophobic |
| F31 | CE2 | PHE- 106 | 4.46 | 0 | Hydrophobic |
| F33 | CE2 | PHE- 106 | 4.44 | 0 | Hydrophobic |
| C2P | CZ | PHE- 106 | 3.99 | 0 | Hydrophobic |
| C20 | CZ | PHE- 106 | 3.96 | 0 | Hydrophobic |
| C22 | CE2 | PHE- 106 | 4.45 | 0 | Hydrophobic |
| O21 | CA | CA- 186 | 2.79 | 0 | Metal Acceptor |
