sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.910 Å
X-ray
1997-09-04
| Name: | Phospholipase A2 |
|---|---|
| ID: | PA21B_BOVIN |
| AC: | P00593 |
| Organism: | Bos taurus |
| Reign: | Eukaryota |
| TaxID: | 9913 |
| EC Number: | 3.1.1.4 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.045 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | CA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.461 | 253.125 |
| % Hydrophobic | % Polar |
|---|---|
| 60.00 | 40.00 |
| According to VolSite | |
| HET Code: | GLE |
|---|---|
| Formula: | C16H31F3O6P |
| Molecular weight: | 407.383 g/mol |
| DrugBank ID: | DB07836 |
| Buried Surface Area: | 54.18 % |
| 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: | 0 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| 33.9062 | 1.82323 | 65.5556 |
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 |
| F33 | CD2 | LEU- 2 | 4.48 | 0 | Hydrophobic |
| C31 | CE2 | PHE- 5 | 3.5 | 0 | Hydrophobic |
| F33 | CD2 | PHE- 5 | 4.44 | 0 | Hydrophobic |
| F32 | CD1 | ILE- 9 | 3.29 | 0 | Hydrophobic |
| F32 | CB | PRO- 18 | 3.28 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 19 | 4.21 | 0 | Hydrophobic |
| F31 | CD2 | LEU- 19 | 3.42 | 0 | Hydrophobic |
| F32 | CB | PHE- 22 | 3.41 | 0 | Hydrophobic |
| F31 | CB | ASN- 23 | 3.58 | 0 | Hydrophobic |
| C2P | CB | CYS- 29 | 4.43 | 0 | Hydrophobic |
| O22 | N | GLY- 30 | 2.86 | 146.54 | H-Bond (Protein Donor) |
| C1 | CD1 | LEU- 31 | 3.67 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 31 | 3.59 | 0 | Hydrophobic |
| C2P | CB | CYS- 45 | 3.54 | 0 | Hydrophobic |
| C2P | CB | HIS- 48 | 4.48 | 0 | Hydrophobic |
| C1 | CE1 | TYR- 69 | 3.99 | 0 | Hydrophobic |
| O2 | OH | TYR- 69 | 2.84 | 174.95 | H-Bond (Protein Donor) |
| F32 | CE2 | PHE- 106 | 4.32 | 0 | Hydrophobic |
| C2P | CZ | PHE- 106 | 3.87 | 0 | Hydrophobic |
| O22 | CA | CA- 124 | 2.32 | 0 | Metal Acceptor |
