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
2010-09-28
| Name: | Uridine phosphorylase 2 |
|---|---|
| ID: | UPP2_HUMAN |
| AC: | O95045 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.4.2.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 14 % |
| D | 86 % |
| B-Factor: | 32.929 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.790 | 799.875 |
| % Hydrophobic | % Polar |
|---|---|
| 42.62 | 57.38 |
| According to VolSite | |
| HET Code: | BAU |
|---|---|
| Formula: | C14H16N2O4 |
| Molecular weight: | 276.288 g/mol |
| DrugBank ID: | DB07437 |
| Buried Surface Area: | 75.67 % |
| Polar Surface area: | 78.87 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 15.1595 | 14.1698 | 50.3442 |
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 |
| CE2 | CD2 | TYR- 41 | 3.21 | 0 | Hydrophobic |
| CZ | CB | TYR- 41 | 4.14 | 0 | Hydrophobic |
| OAC | NE2 | HIS- 42 | 3.1 | 162.32 | H-Bond (Protein Donor) |
| CAJ | SD | MET- 116 | 3.52 | 0 | Hydrophobic |
| CAK | CE1 | PHE- 219 | 3.59 | 0 | Hydrophobic |
| OAB | NE2 | GLN- 223 | 2.79 | 163.05 | H-Bond (Protein Donor) |
| NAN | OE1 | GLN- 223 | 2.61 | 162.11 | H-Bond (Ligand Donor) |
| OAA | NH1 | ARG- 225 | 3.44 | 121.79 | H-Bond (Protein Donor) |
| CAM | CB | GLU- 254 | 4.02 | 0 | Hydrophobic |
| CAK | SD | MET- 255 | 4.25 | 0 | Hydrophobic |
| CAL | CD1 | LEU- 278 | 3.85 | 0 | Hydrophobic |
| CE1 | CD1 | LEU- 279 | 4.45 | 0 | Hydrophobic |
| CD1 | CD2 | LEU- 279 | 3.77 | 0 | Hydrophobic |
| CE1 | CG1 | ILE- 287 | 3.63 | 0 | Hydrophobic |
| CE2 | CD1 | ILE- 287 | 3.72 | 0 | Hydrophobic |
