2.500 Å
X-ray
2003-06-19
| Name: | Purine nucleoside phosphorylase DeoD-type |
|---|---|
| ID: | DEOD_ECO57 |
| AC: | P0ABP9 |
| Organism: | Escherichia coli O157:H7 |
| Reign: | Bacteria |
| TaxID: | 83334 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 27.074 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.303 | 587.250 |
| % Hydrophobic | % Polar |
|---|---|
| 48.28 | 51.72 |
| According to VolSite | |

| HET Code: | TBN |
|---|---|
| Formula: | C11H14N4O4 |
| Molecular weight: | 266.253 g/mol |
| DrugBank ID: | DB03172 |
| Buried Surface Area: | 65.32 % |
| Polar Surface area: | 126.65 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| 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 |
|---|---|---|
| 51.1862 | 50.6814 | 27.8914 |
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' | CG | MET- 64 | 4.26 | 0 | Hydrophobic |
| C5' | SD | MET- 64 | 3.59 | 0 | Hydrophobic |
| C5' | CD2 | PHE- 159 | 3.76 | 0 | Hydrophobic |
| C2' | CB | GLU- 179 | 4.28 | 0 | Hydrophobic |
| C5' | SD | MET- 180 | 4.24 | 0 | Hydrophobic |
| C2' | CB | MET- 180 | 3.76 | 0 | Hydrophobic |
| C3' | SD | MET- 180 | 3.9 | 0 | Hydrophobic |
| O2' | N | MET- 180 | 2.84 | 136.78 | H-Bond (Protein Donor) |
| O3' | OE2 | GLU- 181 | 2.9 | 155.42 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 181 | 2.92 | 128.22 | H-Bond (Ligand Donor) |
| N6 | OD2 | ASP- 204 | 2.98 | 142.04 | H-Bond (Ligand Donor) |