sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.560 Å
X-ray
2012-01-13
| Name: | Purine nucleoside phosphorylase DeoD-type |
|---|---|
| ID: | DEOD_BACSU |
| AC: | O34925 |
| Organism: | Bacillus subtilis |
| Reign: | Bacteria |
| TaxID: | 224308 |
| EC Number: | 2.4.2.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 15 % |
| B | 85 % |
| B-Factor: | 19.854 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.006 | 1194.750 |
| % Hydrophobic | % Polar |
|---|---|
| 42.66 | 57.34 |
| According to VolSite | |
| HET Code: | 2FA |
|---|---|
| Formula: | C10H12FN5O4 |
| Molecular weight: | 285.232 g/mol |
| DrugBank ID: | DB04441 |
| Buried Surface Area: | 70.32 % |
| 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 |
|---|---|---|
| 49.6797 | 21.4666 | 4.3539 |
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 | 2.66 | 162.77 | H-Bond (Ligand Donor) |
| C5' | SD | MET- 64 | 4.28 | 0 | Hydrophobic |
| F | CB | ALA- 156 | 4.17 | 0 | Hydrophobic |
| C5' | CE1 | PHE- 159 | 3.66 | 0 | Hydrophobic |
| F | CD1 | PHE- 159 | 3.33 | 0 | Hydrophobic |
| F | CG2 | VAL- 177 | 3.55 | 0 | Hydrophobic |
| C2' | CB | GLU- 178 | 4.02 | 0 | Hydrophobic |
| C5' | SD | MET- 179 | 4.08 | 0 | Hydrophobic |
| F | CG | MET- 179 | 3.57 | 0 | Hydrophobic |
| C2' | CG | MET- 179 | 4.12 | 0 | Hydrophobic |
| C3' | SD | MET- 179 | 3.88 | 0 | Hydrophobic |
| O3' | OE2 | GLU- 180 | 2.77 | 159.72 | H-Bond (Ligand Donor) |
| N7 | OG | SER- 202 | 2.74 | 142.76 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 203 | 3.34 | 144.64 | H-Bond (Ligand Donor) |
