sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.650 Å
X-ray
2011-07-28
| Name: | Deoxyuridine 5'-triphosphate nucleotidohydrolase |
|---|---|
| ID: | Q8II92_PLAF7 |
| AC: | Q8II92 |
| Organism: | Plasmodium falciparum |
| Reign: | Eukaryota |
| TaxID: | 36329 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 74 % |
| C | 26 % |
| B-Factor: | 20.278 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.517 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 34.11 | 65.89 |
| According to VolSite | |
| HET Code: | DU3 |
|---|---|
| Formula: | C22H24N3O4 |
| Molecular weight: | 394.444 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.21 % |
| Polar Surface area: | 95.48 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 10.5627 | 45.7472 | -1.75814 |
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 |
| C22 | CB | PHE- 46 | 3.92 | 0 | Hydrophobic |
| C29 | CB | SER- 92 | 3.91 | 0 | Hydrophobic |
| C28 | CB | SER- 92 | 3.66 | 0 | Hydrophobic |
| C28 | CB | SER- 95 | 4.1 | 0 | Hydrophobic |
| O4 | ND2 | ASN- 103 | 3.01 | 171.82 | H-Bond (Protein Donor) |
| C1' | CD1 | ILE- 108 | 3.82 | 0 | Hydrophobic |
| C1' | CE2 | TYR- 112 | 3.59 | 0 | Hydrophobic |
| C2' | CD1 | TYR- 112 | 3.76 | 0 | Hydrophobic |
| C4' | CE1 | TYR- 112 | 3.71 | 0 | Hydrophobic |
| O2 | N | ILE- 117 | 2.9 | 168.04 | H-Bond (Protein Donor) |
| N3 | O | ILE- 117 | 2.72 | 150.66 | H-Bond (Ligand Donor) |
| C26 | CG2 | ILE- 117 | 3.72 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 117 | 3.59 | 0 | Hydrophobic |
| C27 | CB | ALA- 119 | 3.67 | 0 | Hydrophobic |
| O4 | O | HOH- 335 | 2.75 | 152.79 | H-Bond (Protein Donor) |
