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
2014-06-18
| Name: | Purine nucleoside phosphorylase DeoD-type |
|---|---|
| ID: | DEOD_ECOLI |
| AC: | P0ABP8 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 14 % |
| C | 86 % |
| B-Factor: | 16.804 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.252 | 772.875 |
| % Hydrophobic | % Polar |
|---|---|
| 44.10 | 55.90 |
| According to VolSite | |
| HET Code: | FMC |
|---|---|
| Formula: | C10H13N5O4 |
| Molecular weight: | 267.241 g/mol |
| DrugBank ID: | DB02281 |
| Buried Surface Area: | 68.87 % |
| Polar Surface area: | 150.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -8.02005 | 80.8795 | 84.8897 |
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 | 2.58 | 157.41 | H-Bond (Protein Donor) |
| C3' | CG | MET- 64 | 4.24 | 0 | Hydrophobic |
| C5' | SD | MET- 64 | 3.7 | 0 | Hydrophobic |
| N8 | OG | SER- 90 | 2.7 | 154.13 | H-Bond (Protein Donor) |
| C5' | CE2 | PHE- 159 | 3.72 | 0 | Hydrophobic |
| C2' | CB | GLU- 179 | 4.13 | 0 | Hydrophobic |
| C2' | CG | MET- 180 | 3.78 | 0 | Hydrophobic |
| C3' | SD | MET- 180 | 3.81 | 0 | Hydrophobic |
| C5' | SD | MET- 180 | 4.1 | 0 | Hydrophobic |
| O2' | N | MET- 180 | 3.01 | 122.84 | H-Bond (Protein Donor) |
| O2' | OE1 | GLU- 181 | 2.57 | 136.73 | H-Bond (Ligand Donor) |
| O3' | OE2 | GLU- 181 | 2.55 | 166.77 | H-Bond (Ligand Donor) |
| N6 | OD1 | ASP- 204 | 3.37 | 168.56 | H-Bond (Ligand Donor) |
