sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.740 Å
X-ray
2006-08-22
| Name: | Purine nucleoside phosphorylase, putative |
|---|---|
| ID: | A2E7Y6_TRIVA |
| AC: | A2E7Y6 |
| Organism: | Trichomonas vaginalis |
| Reign: | Eukaryota |
| TaxID: | 5722 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 13 % |
| B | 87 % |
| B-Factor: | 54.942 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.748 | 600.750 |
| % Hydrophobic | % Polar |
|---|---|
| 47.19 | 52.81 |
| According to VolSite | |
| HET Code: | UA2 |
|---|---|
| Formula: | C11H16N5O3 |
| Molecular weight: | 266.276 g/mol |
| DrugBank ID: | DB11676 |
| Buried Surface Area: | 74.35 % |
| Polar Surface area: | 144.89 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -86.047 | 17.7992 | 18.0382 |
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 |
| O5' | NE2 | HIS- 4 | 3.22 | 173.13 | H-Bond (Protein Donor) |
| C5' | SD | MET- 64 | 3.41 | 0 | Hydrophobic |
| C3' | SD | MET- 64 | 4.25 | 0 | Hydrophobic |
| N4' | OG1 | THR- 90 | 3.32 | 125.23 | H-Bond (Ligand Donor) |
| C5' | CE1 | PHE- 159 | 4.36 | 0 | Hydrophobic |
| C2' | CB | GLU- 179 | 4.21 | 0 | Hydrophobic |
| C3' | SD | MET- 180 | 3.73 | 0 | Hydrophobic |
| C2' | CG | MET- 180 | 3.67 | 0 | Hydrophobic |
| O2' | N | MET- 180 | 2.96 | 128.8 | H-Bond (Protein Donor) |
| O3' | OE1 | GLU- 181 | 2.58 | 161.86 | H-Bond (Ligand Donor) |
| O3' | OE2 | GLU- 181 | 3.32 | 127.82 | H-Bond (Ligand Donor) |
| O3' | OE2 | GLU- 181 | 3.32 | 121.83 | H-Bond (Protein Donor) |
| O2' | OE2 | GLU- 181 | 2.6 | 164.39 | H-Bond (Protein Donor) |
| N7 | OD2 | ASP- 204 | 2.85 | 161.16 | H-Bond (Ligand Donor) |
| N6 | OD1 | ASP- 204 | 3.04 | 152.24 | H-Bond (Ligand Donor) |
