sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
1990-09-01
| 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: | 16.874 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | CA |
| Ligandability | Volume (Å3) |
|---|---|
| 1.041 | 583.875 |
| % Hydrophobic | % Polar |
|---|---|
| 54.91 | 45.09 |
| According to VolSite | |
| HET Code: | DHG |
|---|---|
| Formula: | C20H41NO6P |
| Molecular weight: | 422.516 g/mol |
| DrugBank ID: | DB07657 |
| Buried Surface Area: | 66.7 % |
| Polar Surface area: | 117.73 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 20 |
| X | Y | Z |
|---|---|---|
| -21.0266 | -22.1767 | -14.6457 |
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 |
| C12 | CG | LEU- 2 | 3.65 | 0 | Hydrophobic |
| CH3 | CD1 | LEU- 2 | 4.33 | 0 | Hydrophobic |
| C3 | CE2 | PHE- 5 | 4.21 | 0 | Hydrophobic |
| C5 | CE2 | PHE- 5 | 4.17 | 0 | Hydrophobic |
| C10 | CD2 | PHE- 5 | 4.01 | 0 | Hydrophobic |
| C9 | CG | ARG- 6 | 4.34 | 0 | Hydrophobic |
| C10 | CB | ARG- 6 | 3.91 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 9 | 4.36 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 9 | 3.89 | 0 | Hydrophobic |
| C7 | CB | PRO- 18 | 4.48 | 0 | Hydrophobic |
| C9 | CB | PRO- 18 | 4.36 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 19 | 4 | 0 | Hydrophobic |
| C6 | CB | PHE- 22 | 3.29 | 0 | Hydrophobic |
| C4 | CB | CYS- 29 | 4.08 | 0 | Hydrophobic |
| O1 | N | GLY- 30 | 2.68 | 142.65 | H-Bond (Protein Donor) |
| CH6 | CB | TRP- 31 | 4.33 | 0 | Hydrophobic |
| O2P | N | GLY- 32 | 2.66 | 151.17 | H-Bond (Protein Donor) |
| C2 | CB | CYS- 45 | 3.75 | 0 | Hydrophobic |
| C3 | SG | CYS- 45 | 3.78 | 0 | Hydrophobic |
| C2 | CB | HIS- 48 | 4.13 | 0 | Hydrophobic |
| N | ND1 | HIS- 48 | 2.96 | 164.92 | H-Bond (Ligand Donor) |
| CH1 | CD2 | TYR- 52 | 3.61 | 0 | Hydrophobic |
| CH3 | CE2 | TYR- 52 | 4.3 | 0 | Hydrophobic |
| CG1 | CB | TYR- 52 | 4.23 | 0 | Hydrophobic |
| O1P | OH | TYR- 69 | 2.6 | 175.34 | H-Bond (Protein Donor) |
| C6 | CE2 | PHE- 106 | 4.29 | 0 | Hydrophobic |
| C3 | CZ | PHE- 106 | 3.61 | 0 | Hydrophobic |
| O1 | CA | CA- 125 | 2.57 | 0 | Metal Acceptor |
| O2P | CA | CA- 125 | 2.35 | 0 | Metal Acceptor |
