sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.180 Å
X-ray
2013-03-12
| 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: | 47.184 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.990 | 1009.125 |
| % Hydrophobic | % Polar |
|---|---|
| 52.51 | 47.49 |
| According to VolSite | |
| HET Code: | 1NN |
|---|---|
| Formula: | C19H22FN5O2S2 |
| Molecular weight: | 435.539 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.11 % |
| 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: | 9 |
| X | Y | Z |
|---|---|---|
| -31.8923 | 11.1414 | -3.29062 |
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 |
| NAD | OE1 | GLU- 53 | 3.24 | 147.57 | H-Bond (Ligand Donor) |
| NAD | OE2 | GLU- 53 | 3.25 | 134.38 | H-Bond (Ligand Donor) |
| CAA | CG1 | VAL- 55 | 4.07 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 55 | 3.98 | 0 | Hydrophobic |
| CAK | CD1 | LEU- 82 | 3.64 | 0 | Hydrophobic |
| CAW | CE | MET- 85 | 4.46 | 0 | Hydrophobic |
| SAT | CE | MET- 85 | 3.8 | 0 | Hydrophobic |
| CAK | CE | MET- 85 | 4.46 | 0 | Hydrophobic |
| SAS | CE | MET- 85 | 4.21 | 0 | Hydrophobic |
| CAK | CE1 | TYR- 86 | 4.28 | 0 | Hydrophobic |
| SAT | CE1 | TYR- 86 | 3.31 | 0 | Hydrophobic |
| CAZ | CB | PRO- 89 | 4 | 0 | Hydrophobic |
| CAB | CG | PRO- 89 | 3.93 | 0 | Hydrophobic |
| CAY | CG | PRO- 89 | 3.69 | 0 | Hydrophobic |
| CAK | CZ | PHE- 96 | 4.4 | 0 | Hydrophobic |
| SAS | CE2 | PHE- 96 | 4.47 | 0 | Hydrophobic |
| N1 | NE2 | GLN- 97 | 3.15 | 158.3 | H-Bond (Protein Donor) |
| NAC | OE1 | GLN- 97 | 2.93 | 168.89 | H-Bond (Ligand Donor) |
| NAC | OD1 | ASP- 133 | 2.88 | 151.9 | H-Bond (Ligand Donor) |
| CAM | CD2 | PHE- 137 | 4.27 | 0 | Hydrophobic |
| SAS | CB | PHE- 137 | 3.7 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 137 | 3.88 | 0 | Aromatic Face/Face |
| CAI | CD2 | LEU- 141 | 4.15 | 0 | Hydrophobic |
| SAS | CD1 | LEU- 141 | 4.27 | 0 | Hydrophobic |
| CAL | CD2 | LEU- 141 | 3.65 | 0 | Hydrophobic |
| CAJ | CB | SER- 144 | 3.8 | 0 | Hydrophobic |
| CAL | CE1 | TYR- 204 | 3.41 | 0 | Hydrophobic |
