sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2012-05-15
| Name: | Cyclin-dependent kinase 8 |
|---|---|
| ID: | CDK8_HUMAN |
| AC: | P49336 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.22 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 45.647 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.912 | 415.125 |
| % Hydrophobic | % Polar |
|---|---|
| 58.54 | 41.46 |
| According to VolSite | |
| HET Code: | 0SQ |
|---|---|
| Formula: | C15H20N4O |
| Molecular weight: | 272.345 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.61 % |
| Polar Surface area: | 72.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 38.6299 | 56.5484 | 62.6263 |
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 |
| C20 | CE1 | TYR- 32 | 4.49 | 0 | Hydrophobic |
| C20 | CB | SER- 62 | 3.51 | 0 | Hydrophobic |
| C15 | CG | ARG- 65 | 4.44 | 0 | Hydrophobic |
| N13 | OE2 | GLU- 66 | 3.4 | 132.15 | H-Bond (Ligand Donor) |
| N11 | OE2 | GLU- 66 | 3.09 | 148.36 | H-Bond (Ligand Donor) |
| C10 | CG | GLU- 66 | 3.81 | 0 | Hydrophobic |
| C17 | CB | GLU- 66 | 3.82 | 0 | Hydrophobic |
| C15 | CB | GLU- 66 | 3.53 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 70 | 4.24 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 73 | 3.68 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 78 | 4.03 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 142 | 4.18 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 142 | 4.42 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 142 | 4.21 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 147 | 4.3 | 0 | Hydrophobic |
| C7 | CG2 | ILE- 171 | 3.76 | 0 | Hydrophobic |
| O14 | N | ASP- 173 | 3.17 | 166.65 | H-Bond (Protein Donor) |
| C19 | CB | ASP- 173 | 3.86 | 0 | Hydrophobic |
