2.900 Å
X-ray
2007-02-08
| 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: | 28.458 |
|---|---|
| Number of residues: | 14 |
| Including | |
| Standard Amino Acids: | 13 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.913 | 469.125 |
| % Hydrophobic | % Polar |
|---|---|
| 61.15 | 38.85 |
| According to VolSite | |

| HET Code: | NIM |
|---|---|
| Formula: | C13H12N2O5S |
| Molecular weight: | 308.310 g/mol |
| DrugBank ID: | DB04743 |
| Buried Surface Area: | 25.96 % |
| Polar Surface area: | 109.6 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 33.4679 | 5.105 | -9.58038 |
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 |
| C1 | CD2 | LEU- 2 | 3.3 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 2 | 4.48 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 2 | 3.62 | 0 | Hydrophobic |
| C4 | CG1 | ILE- 19 | 4.41 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 19 | 3.2 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 19 | 3.93 | 0 | Hydrophobic |
| C4 | CB | SER- 23 | 3.79 | 0 | Hydrophobic |
| O2 | NZ | LYS- 69 | 3.24 | 166.99 | H-Bond (Protein Donor) |
| C1 | CD | LYS- 69 | 4 | 0 | Hydrophobic |