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
2001-10-30
| 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 | 88 % |
| D | 12 % |
| B-Factor: | 17.461 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.686 | 432.000 |
| % Hydrophobic | % Polar |
|---|---|
| 51.56 | 48.44 |
| According to VolSite | |
| HET Code: | FM2 |
|---|---|
| Formula: | C11H16N5O4 |
| Molecular weight: | 282.276 g/mol |
| DrugBank ID: | DB03986 |
| Buried Surface Area: | 71.09 % |
| Polar Surface area: | 141.39 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 144.685 | 66.9345 | 63.6939 |
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 | 2.68 | 165.83 | H-Bond (Protein Donor) |
| C3' | CG | MET- 64 | 4.16 | 0 | Hydrophobic |
| C5' | SD | MET- 64 | 3.66 | 0 | Hydrophobic |
| C5' | CD1 | ILE- 71 | 4.36 | 0 | Hydrophobic |
| N8 | OG | SER- 90 | 2.83 | 162.84 | H-Bond (Ligand Donor) |
| C5' | CD2 | PHE- 159 | 3.85 | 0 | Hydrophobic |
| C11 | CE2 | PHE- 159 | 4.01 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 178 | 4.13 | 0 | Hydrophobic |
| C2' | CB | GLU- 179 | 4.16 | 0 | Hydrophobic |
| C2' | CG | MET- 180 | 3.72 | 0 | Hydrophobic |
| C3' | SD | MET- 180 | 3.83 | 0 | Hydrophobic |
| C5' | SD | MET- 180 | 4.14 | 0 | Hydrophobic |
| O2' | N | MET- 180 | 2.83 | 133.66 | H-Bond (Protein Donor) |
| O3' | OE2 | GLU- 181 | 2.51 | 162.87 | H-Bond (Protein Donor) |
| N7 | OG | SER- 203 | 3.06 | 132.85 | H-Bond (Ligand Donor) |
| N7 | OD1 | ASP- 204 | 3.37 | 147.32 | H-Bond (Ligand Donor) |
| O5' | O | HOH- 1082 | 2.8 | 156.83 | H-Bond (Protein Donor) |
