sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2012-05-16
| 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: | 41.897 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.176 | 560.250 |
| % Hydrophobic | % Polar |
|---|---|
| 56.63 | 43.37 |
| According to VolSite | |
| HET Code: | 0SO |
|---|---|
| Formula: | C23H35N5O3 |
| Molecular weight: | 429.556 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.69 % |
| Polar Surface area: | 97.28 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 39.8534 | 57.4912 | 145.191 |
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 |
| C31 | CG2 | VAL- 27 | 3.85 | 0 | Hydrophobic |
| C7 | CE2 | TYR- 32 | 3.39 | 0 | Hydrophobic |
| C22 | CD | LYS- 52 | 3.95 | 0 | Hydrophobic |
| C7 | CB | SER- 62 | 3.55 | 0 | Hydrophobic |
| C1 | CG | ARG- 65 | 4.04 | 0 | Hydrophobic |
| N19 | OE2 | GLU- 66 | 3.09 | 131.97 | H-Bond (Ligand Donor) |
| N17 | OE2 | GLU- 66 | 3.02 | 141.59 | H-Bond (Ligand Donor) |
| C4 | CG | GLU- 66 | 3.83 | 0 | Hydrophobic |
| C1 | CB | GLU- 66 | 3.42 | 0 | Hydrophobic |
| C3 | CB | GLU- 66 | 3.69 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 73 | 3.95 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 78 | 4.35 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 78 | 4.14 | 0 | Hydrophobic |
| C22 | CD2 | PHE- 97 | 4.15 | 0 | Hydrophobic |
| C31 | CE1 | TYR- 99 | 3.98 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 142 | 4.2 | 0 | Hydrophobic |
| C14 | CB | HIS- 149 | 4.46 | 0 | Hydrophobic |
| C29 | CD2 | LEU- 158 | 3.45 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 171 | 3.73 | 0 | Hydrophobic |
| O20 | N | ASP- 173 | 3.31 | 168.41 | H-Bond (Protein Donor) |
| C14 | CB | ASP- 173 | 4.19 | 0 | Hydrophobic |
| C6 | CB | ASP- 173 | 3.77 | 0 | Hydrophobic |
| C30 | SD | MET- 174 | 4.18 | 0 | Hydrophobic |
| C29 | CE | MET- 174 | 4.05 | 0 | Hydrophobic |
| C31 | CD | ARG- 356 | 4.16 | 0 | Hydrophobic |
