sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.770 Å
X-ray
2011-02-08
| Name: | Basic phospholipase A2 homolog piratoxin-1 |
|---|---|
| ID: | PA2H1_BOTPI |
| AC: | P58399 |
| Organism: | Bothrops pirajai |
| Reign: | Eukaryota |
| TaxID: | 113192 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 85 % |
| B | 15 % |
| B-Factor: | 31.346 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.261 | 337.500 |
| % Hydrophobic | % Polar |
|---|---|
| 68.00 | 32.00 |
| According to VolSite | |
| HET Code: | ROA |
|---|---|
| Formula: | C18H15O8 |
| Molecular weight: | 359.307 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 35.28 % |
| Polar Surface area: | 147.35 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 3.37012 | 21.5215 | -16.2716 |
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 |
| OAY | O | PHE- 3 | 3.05 | 125.58 | H-Bond (Ligand Donor) |
| CAU | CD | LYS- 7 | 4.05 | 0 | Hydrophobic |
| CAN | CE | LYS- 7 | 3.96 | 0 | Hydrophobic |
| CAV | CB | LYS- 7 | 3.84 | 0 | Hydrophobic |
| CAS | CG | LYS- 7 | 4.24 | 0 | Hydrophobic |
| OAQ | NZ | LYS- 7 | 3.4 | 158.03 | H-Bond (Protein Donor) |
| CAT | CD2 | LEU- 10 | 4.33 | 0 | Hydrophobic |
| CAA | CD2 | LEU- 10 | 3.62 | 0 | Hydrophobic |
| CAE | CG | LEU- 10 | 4.08 | 0 | Hydrophobic |
| CAB | CD1 | LEU- 10 | 3.86 | 0 | Hydrophobic |
| CAD | CG | GLN- 11 | 4.36 | 0 | Hydrophobic |
| CAT | CD1 | LEU- 121 | 4.21 | 0 | Hydrophobic |
| CAW | CG | PRO- 123 | 4.01 | 0 | Hydrophobic |
