sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.890 Å
X-ray
2013-03-12
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.020 | 8.020 | 8.020 | 0.000 | 8.020 | 1 |
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 41.299 |
|---|---|
| Number of residues: | 19 |
| Including | |
| Standard Amino Acids: | 18 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.127 | 1282.500 |
| % Hydrophobic | % Polar |
|---|---|
| 49.74 | 50.26 |
| According to VolSite | |
| HET Code: | 1NO |
|---|---|
| Formula: | C18H20FN5O2S2 |
| Molecular weight: | 421.512 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 40.19 % |
| Polar Surface area: | 162.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -35.967 | -15.8211 | -22.6599 |
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 |
| SAZ | CD1 | ILE- 30 | 4.32 | 0 | Hydrophobic |
| CAO | CD1 | ILE- 30 | 3.79 | 0 | Hydrophobic |
| C5 | CB | SER- 59 | 3.93 | 0 | Hydrophobic |
| SAI | CD1 | LEU- 82 | 4.12 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 82 | 4.33 | 0 | Hydrophobic |
| CAJ | CE1 | TYR- 86 | 3.94 | 0 | Hydrophobic |
| SAI | CD1 | TYR- 86 | 3.77 | 0 | Hydrophobic |
| CAL | CZ | TYR- 86 | 3.62 | 0 | Hydrophobic |
| C5 | CB | GLU- 196 | 3.94 | 0 | Hydrophobic |
| CAJ | CG | GLU- 197 | 3.65 | 0 | Hydrophobic |
| NAA | OE2 | GLU- 197 | 2.96 | 174.79 | H-Bond (Ligand Donor) |
| SAZ | CG1 | ILE- 200 | 3.79 | 0 | Hydrophobic |
| CAO | CD1 | ILE- 200 | 4.04 | 0 | Hydrophobic |
| CAJ | CD1 | ILE- 200 | 4.21 | 0 | Hydrophobic |
| CAT | CG1 | ILE- 200 | 4.11 | 0 | Hydrophobic |
| CAW | CG | PRO- 201 | 3.94 | 0 | Hydrophobic |
