sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2010-11-25
| 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 |
|---|---|
| A | 75 % |
| C | 25 % |
| B-Factor: | 17.456 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.578 | 270.000 |
| % Hydrophobic | % Polar |
|---|---|
| 52.50 | 47.50 |
| According to VolSite | |
| HET Code: | MKH |
|---|---|
| Formula: | C24H27N3O5S |
| Molecular weight: | 469.553 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.08 % |
| Polar Surface area: | 115.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 6.22636 | 11.0832 | -17.1276 |
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 |
| C23 | CG2 | VAL- 65 | 3.85 | 0 | Hydrophobic |
| C29 | CG1 | VAL- 65 | 3.75 | 0 | Hydrophobic |
| C32 | CB | SER- 86 | 3.7 | 0 | Hydrophobic |
| C33 | CB | ALA- 90 | 3.58 | 0 | Hydrophobic |
| C25 | CB | ALA- 90 | 4.07 | 0 | Hydrophobic |
| C26 | CG | LYS- 91 | 3.72 | 0 | Hydrophobic |
| C31 | CB | ALA- 98 | 4.28 | 0 | Hydrophobic |
| O1 | N | GLY- 99 | 2.92 | 127.92 | H-Bond (Protein Donor) |
| C9 | CG1 | ILE- 101 | 4.43 | 0 | Hydrophobic |
| C9 | CE2 | TYR- 105 | 3.41 | 0 | Hydrophobic |
| C10 | CE1 | TYR- 105 | 3.5 | 0 | Hydrophobic |
| C11 | CZ | TYR- 105 | 3.59 | 0 | Hydrophobic |
| N3 | O | GLY- 110 | 2.71 | 156 | H-Bond (Ligand Donor) |
| O8 | N | GLY- 110 | 2.9 | 174.63 | H-Bond (Protein Donor) |
| C31 | CG2 | VAL- 112 | 3.45 | 0 | Hydrophobic |
| O1 | O | HOH- 173 | 2.8 | 180 | H-Bond (Protein Donor) |
