sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.200 Å
X-ray
2014-05-17
| 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: | 14.362 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.067 | 492.750 |
| % Hydrophobic | % Polar |
|---|---|
| 60.27 | 39.73 |
| According to VolSite | |
| HET Code: | HC4 |
|---|---|
| Formula: | C9H7O3 |
| Molecular weight: | 163.150 g/mol |
| DrugBank ID: | DB04066 |
| Buried Surface Area: | 53.03 % |
| Polar Surface area: | 60.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 2.44708 | -19.7339 | -5.10375 |
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' | CE2 | PHE- 5 | 3.29 | 0 | Hydrophobic |
| C4' | CB | CYS- 45 | 4.1 | 0 | Hydrophobic |
| C3' | SG | CYS- 45 | 3.7 | 0 | Hydrophobic |
| C4' | CB | HIS- 48 | 4.37 | 0 | Hydrophobic |
| O4' | OD1 | ASP- 49 | 2.79 | 171.25 | H-Bond (Ligand Donor) |
