sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2004-05-31
| Name: | Uridine phosphorylase |
|---|---|
| ID: | UDP_ECOLI |
| AC: | P12758 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 2.4.2.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 87 % |
| B | 13 % |
| B-Factor: | 24.569 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.486 | 907.875 |
| % Hydrophobic | % Polar |
|---|---|
| 39.78 | 60.22 |
| According to VolSite | |
| HET Code: | 5UD |
|---|---|
| Formula: | C9H11FN2O6 |
| Molecular weight: | 262.192 g/mol |
| DrugBank ID: | DB01629 |
| Buried Surface Area: | 77.69 % |
| Polar Surface area: | 119.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 54.8955 | 26.9359 | 34.0745 |
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- 8 | 2.64 | 167.4 | H-Bond (Ligand Donor) |
| C3' | CG2 | ILE- 69 | 4.27 | 0 | Hydrophobic |
| C5' | CD1 | ILE- 69 | 4.22 | 0 | Hydrophobic |
| C5' | CD1 | PHE- 162 | 3.6 | 0 | Hydrophobic |
| N3 | OE1 | GLN- 166 | 2.81 | 171.52 | H-Bond (Ligand Donor) |
| O2 | NE2 | GLN- 166 | 2.94 | 143.3 | H-Bond (Protein Donor) |
| O4 | NH2 | ARG- 168 | 2.9 | 170.34 | H-Bond (Protein Donor) |
| C2' | CB | GLU- 196 | 4.24 | 0 | Hydrophobic |
| C2' | CG | MET- 197 | 3.78 | 0 | Hydrophobic |
| C3' | SD | MET- 197 | 3.71 | 0 | Hydrophobic |
| C5' | SD | MET- 197 | 4.25 | 0 | Hydrophobic |
| O2' | N | MET- 197 | 2.97 | 153.3 | H-Bond (Protein Donor) |
| O2' | OE1 | GLU- 198 | 3.04 | 148.09 | H-Bond (Protein Donor) |
| O3' | OE1 | GLU- 198 | 3.14 | 137.06 | H-Bond (Protein Donor) |
| F5 | CG1 | ILE- 220 | 3.2 | 0 | Hydrophobic |
| F5 | CG1 | VAL- 221 | 3.31 | 0 | Hydrophobic |
| O4 | O | HOH- 3032 | 2.94 | 175.93 | H-Bond (Protein Donor) |
