sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2010-04-13
| Name: | Deoxycytidine kinase |
|---|---|
| ID: | DCK_HUMAN |
| AC: | P27707 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.1.74 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 30.154 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.844 | 850.500 |
| % Hydrophobic | % Polar |
|---|---|
| 53.17 | 46.83 |
| According to VolSite | |
| HET Code: | AC2 |
|---|---|
| Formula: | C8H11N5O3 |
| Molecular weight: | 225.205 g/mol |
| DrugBank ID: | DB00787 |
| Buried Surface Area: | 58.39 % |
| Polar Surface area: | 114.76 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 10.743 | 20.6732 | 8.81762 |
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 |
| C2' | CD1 | ILE- 30 | 3.68 | 0 | Hydrophobic |
| O6 | NE2 | GLN- 97 | 3.09 | 126.46 | H-Bond (Protein Donor) |
| N1 | OD1 | ASP- 133 | 3.2 | 155.65 | H-Bond (Ligand Donor) |
| C3' | CD2 | PHE- 137 | 3.56 | 0 | Hydrophobic |
| C2' | CE2 | PHE- 137 | 4.37 | 0 | Hydrophobic |
| C3' | CZ | TYR- 204 | 3.61 | 0 | Hydrophobic |
