sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.940 Å
X-ray
2013-06-10
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.100 | 9.100 | 9.100 | 0.000 | 9.100 | 2 |
| 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: | 43.689 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.991 | 715.500 |
| % Hydrophobic | % Polar |
|---|---|
| 55.66 | 44.34 |
| According to VolSite | |
| HET Code: | 1UX |
|---|---|
| Formula: | C22H29N5O3S2 |
| Molecular weight: | 475.627 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.94 % |
| Polar Surface area: | 182.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| -32.0009 | -11.626 | -22.6281 |
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 |
| CAA | CD1 | ILE- 30 | 4.03 | 0 | Hydrophobic |
| CAO | CD1 | ILE- 30 | 4.28 | 0 | Hydrophobic |
| NAE | OE2 | GLU- 53 | 3.44 | 140.69 | H-Bond (Ligand Donor) |
| NAE | OE1 | GLU- 53 | 3.31 | 164.96 | H-Bond (Ligand Donor) |
| C5 | CG2 | VAL- 55 | 4.21 | 0 | Hydrophobic |
| CAL | CD1 | LEU- 82 | 3.62 | 0 | Hydrophobic |
| SAV | CG | MET- 85 | 3.98 | 0 | Hydrophobic |
| CAK | CE | MET- 85 | 4.26 | 0 | Hydrophobic |
| CAL | CE1 | TYR- 86 | 4.15 | 0 | Hydrophobic |
| CAH | CB | TYR- 86 | 4.37 | 0 | Hydrophobic |
| CAB | CG | PRO- 89 | 3.85 | 0 | Hydrophobic |
| CBA | CG | PRO- 89 | 4.25 | 0 | Hydrophobic |
| CAM | CZ | PHE- 96 | 4.08 | 0 | Hydrophobic |
| SAU | CE2 | PHE- 96 | 4.35 | 0 | Hydrophobic |
| N3 | NE2 | GLN- 97 | 2.93 | 160.77 | H-Bond (Protein Donor) |
| NAF | OE1 | GLN- 97 | 3.14 | 169.8 | H-Bond (Ligand Donor) |
| NAF | OD1 | ASP- 133 | 2.72 | 156.67 | H-Bond (Ligand Donor) |
| SAU | CD2 | PHE- 137 | 3.45 | 0 | Hydrophobic |
| CAC | CD2 | LEU- 141 | 4.23 | 0 | Hydrophobic |
| CAN | CD2 | LEU- 141 | 4.09 | 0 | Hydrophobic |
| CAC | CB | SER- 144 | 3.5 | 0 | Hydrophobic |
| OAG | OG | SER- 146 | 3.13 | 139.53 | H-Bond (Ligand Donor) |
| CAC | CE1 | TYR- 204 | 4.03 | 0 | Hydrophobic |
| CAN | CZ | TYR- 204 | 3.94 | 0 | Hydrophobic |
| CAO | CZ | TYR- 204 | 4.21 | 0 | Hydrophobic |
| NAR | OH | TYR- 204 | 2.59 | 156.07 | H-Bond (Protein Donor) |
