sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2008-11-18
| Name: | Purine nucleoside phosphorylase |
|---|---|
| ID: | Q9BMI9_SCHMA |
| AC: | Q9BMI9 |
| Organism: | Schistosoma mansoni |
| Reign: | Eukaryota |
| TaxID: | 6183 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 27.585 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.976 | 732.375 |
| % Hydrophobic | % Polar |
|---|---|
| 39.63 | 60.37 |
| According to VolSite | |
| HET Code: | NOS |
|---|---|
| Formula: | C10H12N4O5 |
| Molecular weight: | 268.226 g/mol |
| DrugBank ID: | DB04335 |
| Buried Surface Area: | 79.27 % |
| Polar Surface area: | 133.75 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -5.22732 | 1.89232 | 29.7991 |
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 |
| C3' | CE2 | TYR- 90 | 4.1 | 0 | Hydrophobic |
| O3' | OH | TYR- 90 | 2.72 | 131.43 | H-Bond (Protein Donor) |
| C1' | CB | ALA- 118 | 3.9 | 0 | Hydrophobic |
| C5' | CG | PHE- 161 | 3.74 | 0 | Hydrophobic |
| C4' | CZ | PHE- 161 | 3.93 | 0 | Hydrophobic |
| C3' | CE1 | PHE- 161 | 3.67 | 0 | Hydrophobic |
| C5' | CE2 | TYR- 202 | 3.74 | 0 | Hydrophobic |
| O5' | OH | TYR- 202 | 2.53 | 164.79 | H-Bond (Ligand Donor) |
| N1 | OE1 | GLU- 203 | 2.55 | 170.86 | H-Bond (Ligand Donor) |
| C2' | CG | MET- 221 | 3.65 | 0 | Hydrophobic |
| C3' | SD | MET- 221 | 3.89 | 0 | Hydrophobic |
| O2' | N | MET- 221 | 2.82 | 149.57 | H-Bond (Protein Donor) |
| O6 | ND2 | ASN- 245 | 2.84 | 164.59 | H-Bond (Protein Donor) |
| O5' | ND1 | HIS- 259 | 2.73 | 160.01 | H-Bond (Protein Donor) |
| O2' | O | HOH- 424 | 2.84 | 179.99 | H-Bond (Protein Donor) |
