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
2007-02-22
| Name: | Basic phospholipase A2 VRV-PL-VIIIa |
|---|---|
| ID: | PA2B8_DABRR |
| AC: | P59071 |
| Organism: | Daboia russelii |
| Reign: | Eukaryota |
| TaxID: | 31159 |
| EC Number: | 3.1.1.4 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 18.235 |
|---|---|
| Number of residues: | 12 |
| Including | |
| Standard Amino Acids: | 12 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.740 | 378.000 |
| % Hydrophobic | % Polar |
|---|---|
| 64.29 | 35.71 |
| According to VolSite | |
| HET Code: | IAC |
|---|---|
| Formula: | C10H8NO2 |
| Molecular weight: | 174.176 g/mol |
| DrugBank ID: | DB07950 |
| Buried Surface Area: | 37.99 % |
| Polar Surface area: | 55.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -21.0791 | 5.26708 | -9.07246 |
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 |
| C4 | CG | LEU- 2 | 4.42 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 2 | 4.37 | 0 | Hydrophobic |
| C | CD2 | LEU- 2 | 3.38 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 2 | 3.59 | 0 | Hydrophobic |
| C4 | CB | ALA- 18 | 4.05 | 0 | Hydrophobic |
| C | CD1 | ILE- 19 | 3.6 | 0 | Hydrophobic |
| C4 | CG1 | ILE- 19 | 3.68 | 0 | Hydrophobic |
| C4 | CB | SER- 23 | 4.27 | 0 | Hydrophobic |
| O2 | NZ | LYS- 69 | 2.78 | 147.9 | H-Bond (Protein Donor) |
| O3 | NZ | LYS- 69 | 2.89 | 141.52 | H-Bond (Protein Donor) |
| O2 | NZ | LYS- 69 | 2.78 | 0 | Ionic (Protein Cationic) |
| O3 | NZ | LYS- 69 | 2.89 | 0 | Ionic (Protein Cationic) |
