sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.240 Å
X-ray
2015-06-25
| Name: | Uridine phosphorylase |
|---|---|
| ID: | Q9K4U1_VIBCL |
| AC: | Q9K4U1 |
| Organism: | Vibrio cholerae |
| Reign: | Bacteria |
| TaxID: | 666 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 15 % |
| D | 85 % |
| B-Factor: | 26.966 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 0.474 | 830.250 |
| % Hydrophobic | % Polar |
|---|---|
| 52.03 | 47.97 |
| According to VolSite | |
| HET Code: | URI |
|---|---|
| Formula: | C9H12N2O6 |
| Molecular weight: | 244.201 g/mol |
| DrugBank ID: | DB02745 |
| Buried Surface Area: | 75.51 % |
| 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 |
|---|---|---|
| -25.8319 | 45.0213 | 18.9175 |
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- 7 | 2.63 | 162.13 | H-Bond (Ligand Donor) |
| C3' | CG2 | ILE- 68 | 4.39 | 0 | Hydrophobic |
| C4' | CG1 | ILE- 68 | 4.45 | 0 | Hydrophobic |
| C5' | CD1 | ILE- 68 | 3.46 | 0 | Hydrophobic |
| C1' | CE1 | PHE- 161 | 4.47 | 0 | Hydrophobic |
| C5' | CD1 | PHE- 161 | 4.03 | 0 | Hydrophobic |
| N3 | OE1 | GLN- 165 | 2.92 | 175.86 | H-Bond (Ligand Donor) |
| O2 | NE2 | GLN- 165 | 2.84 | 163.49 | H-Bond (Protein Donor) |
| C2' | CB | GLU- 195 | 4.29 | 0 | Hydrophobic |
| C2' | CG | MET- 196 | 3.73 | 0 | Hydrophobic |
| C3' | SD | MET- 196 | 3.81 | 0 | Hydrophobic |
| O2' | N | MET- 196 | 3.26 | 136.38 | H-Bond (Protein Donor) |
| O2' | OE1 | GLU- 197 | 2.64 | 148.09 | H-Bond (Ligand Donor) |
| O4 | O | HOH- 408 | 2.95 | 142 | H-Bond (Protein Donor) |
