sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2005-11-16
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 71.355 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.175 | 482.625 |
| % Hydrophobic | % Polar |
|---|---|
| 53.15 | 46.85 |
| According to VolSite | |
| HET Code: | AP9 |
|---|---|
| Formula: | C19H26ClN7O |
| Molecular weight: | 403.909 g/mol |
| DrugBank ID: | DB07379 |
| Buried Surface Area: | 53.44 % |
| Polar Surface area: | 113.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 30.6358 | 21.6578 | 61.4421 |
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 |
| C14 | CB | VAL- 27 | 3.66 | 0 | Hydrophobic |
| C9 | CB | ALA- 41 | 3.83 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 77 | 3.42 | 0 | Hydrophobic |
| C11 | CD1 | PHE- 98 | 3.93 | 0 | Hydrophobic |
| C10 | CG | PHE- 98 | 3.4 | 0 | Hydrophobic |
| N7 | N | VAL- 101 | 3.35 | 160.63 | H-Bond (Protein Donor) |
| N6 | O | VAL- 101 | 3.14 | 129.43 | H-Bond (Ligand Donor) |
| C15 | CB | ASP- 104 | 4.02 | 0 | Hydrophobic |
| CL1 | CB | ASP- 104 | 4.48 | 0 | Hydrophobic |
| C6A | CB | ASP- 104 | 4.05 | 0 | Hydrophobic |
| CL1 | CB | THR- 107 | 3.71 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 152 | 4.47 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 152 | 4.22 | 0 | Hydrophobic |
