sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.480 Å
X-ray
2014-05-20
| Name: | Phospholipase A2 VRV-PL-VIIIa |
|---|---|
| ID: | D0VX11_9SAUR |
| AC: | D0VX11 |
| Organism: | Daboia russellii pulchella |
| Reign: | Eukaryota |
| TaxID: | 97228 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 22.798 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.786 | 384.750 |
| % Hydrophobic | % Polar |
|---|---|
| 63.16 | 36.84 |
| According to VolSite | |
| HET Code: | C0R |
|---|---|
| Formula: | C21H30O4 |
| Molecular weight: | 346.460 g/mol |
| DrugBank ID: | DB04652 |
| Buried Surface Area: | 53.97 % |
| Polar Surface area: | 74.6 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 20.9285 | 5.73967 | -5.81338 |
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 |
| C18 | CG | LEU- 2 | 4.22 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 2 | 4 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 2 | 3.57 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 2 | 3.28 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 3 | 3.23 | 0 | Hydrophobic |
| C17 | CE2 | PHE- 5 | 4.03 | 0 | Hydrophobic |
| C21 | CE2 | PHE- 5 | 3.76 | 0 | Hydrophobic |
| C18 | CD2 | PHE- 5 | 3.57 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 9 | 4.22 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 9 | 3.97 | 0 | Hydrophobic |
| C12 | CB | ALA- 18 | 3.57 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 19 | 3.56 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 19 | 3.66 | 0 | Hydrophobic |
| C9 | CG1 | ILE- 19 | 3.49 | 0 | Hydrophobic |
| C16 | CB | TYR- 22 | 4.01 | 0 | Hydrophobic |
| C16 | CB | SER- 23 | 3.57 | 0 | Hydrophobic |
| C14 | CB | SER- 23 | 3.75 | 0 | Hydrophobic |
| O4 | N | GLY- 30 | 2.69 | 149.51 | H-Bond (Protein Donor) |
| O4 | O | HOH- 332 | 2.93 | 152.41 | H-Bond (Ligand Donor) |
