sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
1998-04-16
| Name: | Uracil phosphoribosyltransferase |
|---|---|
| ID: | UPP_TOXGO |
| AC: | Q26998 |
| Organism: | Toxoplasma gondii |
| Reign: | Eukaryota |
| TaxID: | 5811 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 97 % |
| C | 3 % |
| B-Factor: | 34.754 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.299 | 705.375 |
| % Hydrophobic | % Polar |
|---|---|
| 32.06 | 67.94 |
| According to VolSite | |
| HET Code: | U5P |
|---|---|
| Formula: | C9H11N2O9P |
| Molecular weight: | 322.165 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.3 % |
| Polar Surface area: | 181.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 9.55405 | 68.1913 | 91.947 |
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 |
| O1P | NH2 | ARG- 137 | 3.42 | 147.38 | H-Bond (Protein Donor) |
| O2P | NH2 | ARG- 137 | 2.58 | 120.28 | H-Bond (Protein Donor) |
| O2P | CZ | ARG- 137 | 3.78 | 0 | Ionic (Protein Cationic) |
| O2' | OD1 | ASP- 164 | 3.21 | 159.01 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 164 | 3.42 | 142.24 | H-Bond (Ligand Donor) |
| C1' | CE | MET- 166 | 4.22 | 0 | Hydrophobic |
| C2' | CB | MET- 166 | 3.98 | 0 | Hydrophobic |
| O3P | N | ALA- 168 | 2.96 | 140.48 | H-Bond (Protein Donor) |
| O1P | N | THR- 169 | 3.02 | 154.67 | H-Bond (Protein Donor) |
| O1P | OG1 | THR- 169 | 2.63 | 169.06 | H-Bond (Protein Donor) |
| O3P | N | ALA- 170 | 2.9 | 139.89 | H-Bond (Protein Donor) |
| C5' | CB | SER- 172 | 4.39 | 0 | Hydrophobic |
| O2P | N | SER- 172 | 2.95 | 168.09 | H-Bond (Protein Donor) |
| O4 | N | ILE- 229 | 3.02 | 164.18 | H-Bond (Protein Donor) |
| N3 | O | GLY- 234 | 2.9 | 175.58 | H-Bond (Ligand Donor) |
| O2 | N | PHE- 236 | 3.14 | 137.3 | H-Bond (Protein Donor) |
| O4 | O | HOH- 1002 | 2.65 | 165.23 | H-Bond (Protein Donor) |
