sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2001-06-15
| Name: | Purine nucleoside phosphorylase |
|---|---|
| ID: | PNPH_SULSO |
| AC: | P50389 |
| Organism: | Sulfolobus solfataricus |
| Reign: | Archaea |
| TaxID: | 273057 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 12 % |
| D | 88 % |
| B-Factor: | 29.521 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.550 | 739.125 |
| % Hydrophobic | % Polar |
|---|---|
| 41.55 | 58.45 |
| According to VolSite | |
| HET Code: | ADN |
|---|---|
| Formula: | C10H13N5O4 |
| Molecular weight: | 267.241 g/mol |
| DrugBank ID: | DB00640 |
| Buried Surface Area: | 73.24 % |
| Polar Surface area: | 139.54 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 |
|---|---|---|
| -8.12121 | -10.3849 | 115.691 |
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- 5 | 2.82 | 144.5 | H-Bond (Ligand Donor) |
| C3' | CG2 | ILE- 64 | 4.41 | 0 | Hydrophobic |
| C5' | CE1 | PHE- 160 | 4.04 | 0 | Hydrophobic |
| N1 | OE1 | GLU- 163 | 3 | 158 | H-Bond (Protein Donor) |
| C2' | CB | GLU- 180 | 4.34 | 0 | Hydrophobic |
| C5' | SD | MET- 181 | 4.4 | 0 | Hydrophobic |
| C3' | SD | MET- 181 | 3.9 | 0 | Hydrophobic |
| C2' | CG | MET- 181 | 3.85 | 0 | Hydrophobic |
| O2' | N | MET- 181 | 2.93 | 143.74 | H-Bond (Protein Donor) |
| O2' | OE1 | GLU- 182 | 2.8 | 141.1 | H-Bond (Ligand Donor) |
| N6 | OD2 | ASP- 205 | 3.05 | 155.32 | H-Bond (Ligand Donor) |
