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
2008-06-06
| Name: | Cyclin-dependent kinase 2 |
|---|---|
| ID: | CDK2_HUMAN |
| AC: | P24941 |
| 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: | 53.831 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.013 | 563.625 |
| % Hydrophobic | % Polar |
|---|---|
| 51.50 | 48.50 |
| According to VolSite | |
| HET Code: | RC8 |
|---|---|
| Formula: | C24H29N7O |
| Molecular weight: | 431.533 g/mol |
| DrugBank ID: | DB08463 |
| Buried Surface Area: | 56.12 % |
| Polar Surface area: | 100.78 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 5.22937 | 26.1499 | 25.7385 |
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 |
| C4B | CG | GLU- 8 | 4.25 | 0 | Hydrophobic |
| C3' | CG1 | ILE- 10 | 3.86 | 0 | Hydrophobic |
| C6' | CG2 | ILE- 10 | 3.73 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 18 | 4.2 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 18 | 3.83 | 0 | Hydrophobic |
| C11 | CB | ALA- 31 | 3.65 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 64 | 3.63 | 0 | Hydrophobic |
| C9 | CG | PHE- 80 | 4.34 | 0 | Hydrophobic |
| C10 | CD2 | PHE- 80 | 3.73 | 0 | Hydrophobic |
| C11 | CD1 | PHE- 80 | 3.41 | 0 | Hydrophobic |
| N7 | N | LEU- 83 | 3.4 | 143.8 | H-Bond (Protein Donor) |
| N6 | O | LEU- 83 | 2.89 | 146.02 | H-Bond (Ligand Donor) |
| CA' | CB | GLN- 85 | 4.45 | 0 | Hydrophobic |
| CA' | CD2 | LEU- 134 | 4.38 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 134 | 3.96 | 0 | Hydrophobic |
| C10 | CB | ALA- 144 | 4.13 | 0 | Hydrophobic |
| C14 | CB | ALA- 144 | 4.16 | 0 | Hydrophobic |
| C14 | CB | ASP- 145 | 3.99 | 0 | Hydrophobic |
