sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.310 Å
X-ray
2012-05-15
| Name: | Cyclin-dependent kinase 6 |
|---|---|
| ID: | CDK6_HUMAN |
| AC: | Q00534 |
| 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: | 53.953 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.648 | 502.875 |
| % Hydrophobic | % Polar |
|---|---|
| 47.65 | 52.35 |
| According to VolSite | |
| HET Code: | 4AU |
|---|---|
| Formula: | C12H9N3O |
| Molecular weight: | 211.219 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.55 % |
| Polar Surface area: | 61.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 22.8105 | 34.6783 | -9.23994 |
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 |
| C4 | CD1 | ILE- 19 | 4.22 | 0 | Hydrophobic |
| N7 | O | GLU- 99 | 3.28 | 160.32 | H-Bond (Ligand Donor) |
| N9 | O | VAL- 101 | 2.75 | 153.22 | H-Bond (Ligand Donor) |
| O16 | N | VAL- 101 | 2.96 | 164.57 | H-Bond (Protein Donor) |
| C1 | CB | ASP- 104 | 3.83 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 152 | 4.39 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 152 | 3.81 | 0 | Hydrophobic |
