sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.390 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: | 40.571 |
|---|---|
| Number of residues: | 49 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.933 | 496.125 |
| % Hydrophobic | % Polar |
|---|---|
| 51.02 | 48.98 |
| According to VolSite | |
| HET Code: | 0SS |
|---|---|
| Formula: | C36H50N9O2 |
| Molecular weight: | 640.841 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.1 % |
| Polar Surface area: | 113.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 39.0714 | 56.7661 | 142.413 |
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 |
| C7 | CG2 | VAL- 27 | 3.6 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 35 | 4.28 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 35 | 3.82 | 0 | Hydrophobic |
| C7 | CB | ALA- 50 | 4.29 | 0 | Hydrophobic |
| C47 | CB | SER- 62 | 3.89 | 0 | Hydrophobic |
| C43 | CG | ARG- 65 | 4.38 | 0 | Hydrophobic |
| N30 | OE2 | GLU- 66 | 2.84 | 156.58 | H-Bond (Ligand Donor) |
| N28 | OE2 | GLU- 66 | 3.2 | 124.37 | H-Bond (Ligand Donor) |
| C41 | CG | GLU- 66 | 3.88 | 0 | Hydrophobic |
| C43 | CB | GLU- 66 | 3.56 | 0 | Hydrophobic |
| C39 | CD2 | LEU- 69 | 4.47 | 0 | Hydrophobic |
| C41 | CD2 | LEU- 70 | 4.5 | 0 | Hydrophobic |
| C38 | CD2 | LEU- 70 | 4.14 | 0 | Hydrophobic |
| C38 | CD1 | LEU- 73 | 3.73 | 0 | Hydrophobic |
| C38 | CG1 | VAL- 78 | 3.82 | 0 | Hydrophobic |
| C7 | CE1 | TYR- 99 | 3.71 | 0 | Hydrophobic |
| C16 | CE3 | TRP- 105 | 3.66 | 0 | Hydrophobic |
| C40 | CD1 | LEU- 142 | 4.24 | 0 | Hydrophobic |
| C39 | CD1 | LEU- 142 | 4.34 | 0 | Hydrophobic |
| C38 | CD2 | LEU- 142 | 4.21 | 0 | Hydrophobic |
| C39 | CG1 | VAL- 147 | 4.46 | 0 | Hydrophobic |
| C16 | CB | ALA- 155 | 4.2 | 0 | Hydrophobic |
| C14 | CB | ALA- 155 | 4.03 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 158 | 3.82 | 0 | Hydrophobic |
| C40 | CG2 | ILE- 171 | 3.75 | 0 | Hydrophobic |
| O31 | N | ASP- 173 | 2.99 | 160.96 | H-Bond (Protein Donor) |
| C46 | CB | ASP- 173 | 4.15 | 0 | Hydrophobic |
| C37 | CB | ASP- 173 | 4.36 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 356 | 3.68 | 165.42 | Pi/Cation |
| C3 | CD | ARG- 356 | 3.8 | 0 | Hydrophobic |
| N36 | O | HOH- 614 | 2.8 | 167.48 | H-Bond (Protein Donor) |
| N17 | O | HOH- 633 | 2.73 | 158.61 | H-Bond (Ligand Donor) |
| N24 | O | HOH- 649 | 2.79 | 162.42 | H-Bond (Ligand Donor) |
