sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.230 Å
X-ray
2004-06-01
| 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: | 16.335 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.164 | 502.875 |
| % Hydrophobic | % Polar |
|---|---|
| 66.44 | 33.56 |
| According to VolSite | |
| HET Code: | OIN |
|---|---|
| Formula: | C17H24NO3 |
| Molecular weight: | 290.377 g/mol |
| DrugBank ID: | DB00572 |
| Buried Surface Area: | 48.65 % |
| Polar Surface area: | 50.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 51.365 | 36.6307 | 8.10774 |
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 |
| OH | O | TYR- 28 | 2.69 | 138.75 | H-Bond (Ligand Donor) |
| OH | N | GLY- 30 | 3.24 | 146.71 | H-Bond (Protein Donor) |
| C5 | CB | TRP- 31 | 4.34 | 0 | Hydrophobic |
| C13 | CD2 | TYR- 52 | 3.55 | 0 | Hydrophobic |
| C16 | CD | LYS- 69 | 4.06 | 0 | Hydrophobic |
