sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2010-12-03
| Name: | Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial |
|---|---|
| ID: | DUT_HUMAN |
| AC: | P33316 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.6.1.23 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 26 % |
| C | 74 % |
| B-Factor: | 12.362 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.745 | 280.125 |
| % Hydrophobic | % Polar |
|---|---|
| 55.42 | 44.58 |
| According to VolSite | |
| HET Code: | MSJ |
|---|---|
| Formula: | C17H23N3O5S |
| Molecular weight: | 381.447 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 55.06 % |
| Polar Surface area: | 113.18 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 14.7424 | 47.0542 | 34.9197 |
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 |
| C16 | CG1 | VAL- 65 | 3.67 | 0 | Hydrophobic |
| C13 | CB | SER- 86 | 4.14 | 0 | Hydrophobic |
| C25 | CB | SER- 86 | 4.1 | 0 | Hydrophobic |
| C20 | CB | SER- 86 | 3.84 | 0 | Hydrophobic |
| C20 | CB | ALA- 90 | 3.43 | 0 | Hydrophobic |
| C18 | CB | ALA- 98 | 4.1 | 0 | Hydrophobic |
| O1 | N | GLY- 99 | 2.82 | 130.58 | H-Bond (Protein Donor) |
| C9 | CG1 | ILE- 101 | 4.49 | 0 | Hydrophobic |
| C9 | CZ | TYR- 105 | 3.48 | 0 | Hydrophobic |
| C11 | CZ | TYR- 105 | 3.66 | 0 | Hydrophobic |
| C12 | CE1 | TYR- 105 | 4.33 | 0 | Hydrophobic |
| N3 | O | GLY- 110 | 2.7 | 162.65 | H-Bond (Ligand Donor) |
| O8 | N | GLY- 110 | 2.88 | 174.19 | H-Bond (Protein Donor) |
| C18 | CG2 | VAL- 112 | 3.42 | 0 | Hydrophobic |
| O1 | O | HOH- 183 | 2.73 | 166.36 | H-Bond (Protein Donor) |
