sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2012-05-02
| 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: | 87.793 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.285 | 891.000 |
| % Hydrophobic | % Polar |
|---|---|
| 50.38 | 49.62 |
| According to VolSite | |
| HET Code: | 0RS |
|---|---|
| Formula: | C28H28N7O |
| Molecular weight: | 478.568 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 48.85 % |
| Polar Surface area: | 92.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 6 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 36.8901 | 23.2173 | 9.19422 |
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 |
| C10 | CG2 | ILE- 19 | 3.53 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 27 | 4.1 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 27 | 4.49 | 0 | Hydrophobic |
| C15 | CB | ALA- 41 | 3.74 | 0 | Hydrophobic |
| N7 | NZ | LYS- 43 | 3.3 | 148.95 | H-Bond (Protein Donor) |
| C16 | CG2 | VAL- 77 | 3.83 | 0 | Hydrophobic |
| C16 | CB | PHE- 98 | 4.2 | 0 | Hydrophobic |
| O1 | N | VAL- 101 | 2.97 | 151.39 | H-Bond (Protein Donor) |
| N4 | O | VAL- 101 | 3.13 | 121.26 | H-Bond (Ligand Donor) |
| C9 | CB | ASP- 104 | 3.97 | 0 | Hydrophobic |
| C6 | CG2 | THR- 107 | 3.46 | 0 | Hydrophobic |
| C26 | CB | ASN- 150 | 3.64 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 152 | 4 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 152 | 3.46 | 0 | Hydrophobic |
| C19 | CB | ALA- 162 | 4.29 | 0 | Hydrophobic |
| C27 | CB | ALA- 162 | 3.98 | 0 | Hydrophobic |
| C23 | CB | ASP- 163 | 3.36 | 0 | Hydrophobic |
