sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2004-05-05
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.300 | 5.300 | 5.300 | 0.000 | 5.300 | 1 |
| 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: | 43.613 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.578 | 307.125 |
| % Hydrophobic | % Polar |
|---|---|
| 45.05 | 54.95 |
| According to VolSite | |
| HET Code: | DUX |
|---|---|
| Formula: | C28H25FN2O4 |
| Molecular weight: | 472.507 g/mol |
| DrugBank ID: | DB04685 |
| Buried Surface Area: | 49.97 % |
| Polar Surface area: | 67.87 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 25.6151 | 5.83203 | 7.1114 |
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 | 4.4 | 0 | Hydrophobic |
| C31 | CB | SER- 92 | 4.32 | 0 | Hydrophobic |
| C26 | CB | SER- 92 | 3.38 | 0 | Hydrophobic |
| C26 | CB | SER- 95 | 4.01 | 0 | Hydrophobic |
| C33 | CD | LYS- 96 | 3.59 | 0 | Hydrophobic |
| C34 | CG | LYS- 96 | 4.22 | 0 | Hydrophobic |
| C35 | CD | LYS- 96 | 3.9 | 0 | Hydrophobic |
| O4 | ND2 | ASN- 103 | 3.34 | 171.17 | H-Bond (Protein Donor) |
| C2' | CD1 | TYR- 112 | 3.78 | 0 | Hydrophobic |
| C1' | CE2 | TYR- 112 | 3.63 | 0 | Hydrophobic |
| C4' | CE1 | TYR- 112 | 3.74 | 0 | Hydrophobic |
| N3 | O | ILE- 117 | 2.89 | 143.48 | H-Bond (Ligand Donor) |
| O2 | N | ILE- 117 | 3.23 | 178.66 | H-Bond (Protein Donor) |
| C29 | CG2 | ILE- 117 | 4.31 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 117 | 4.04 | 0 | Hydrophobic |
| C27 | CB | ALA- 119 | 3.5 | 0 | Hydrophobic |
| O4 | O | HOH- 2025 | 2.73 | 168.39 | H-Bond (Protein Donor) |
