sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.400 Å
X-ray
2008-12-29
| 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: | 24.485 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.917 | 553.500 |
| % Hydrophobic | % Polar |
|---|---|
| 62.80 | 37.20 |
| According to VolSite | |
| HET Code: | IMN |
|---|---|
| Formula: | C19H15ClNO4 |
| Molecular weight: | 356.780 g/mol |
| DrugBank ID: | DB00328 |
| Buried Surface Area: | 33.64 % |
| Polar Surface area: | 71.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 51.6771 | 40.1697 | 8.78328 |
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 |
| C6 | CB | ASP- 49 | 4.17 | 0 | Hydrophobic |
| C2 | CB | ASP- 49 | 3.55 | 0 | Hydrophobic |
| C16 | CD2 | TYR- 52 | 3.76 | 0 | Hydrophobic |
| C17 | CD2 | TYR- 52 | 4.06 | 0 | Hydrophobic |
| C | CB | TYR- 52 | 4.13 | 0 | Hydrophobic |
| C16 | CG | LYS- 69 | 3.66 | 0 | Hydrophobic |
| O2 | NZ | LYS- 69 | 2.85 | 0 | Ionic (Protein Cationic) |
| C6 | SG | CYS- 133 | 4.45 | 0 | Hydrophobic |
