sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2010-05-09
| 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 |
|---|---|
| C | 100 % |
| B-Factor: | 41.764 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.015 | 745.875 |
| % Hydrophobic | % Polar |
|---|---|
| 47.96 | 52.04 |
| According to VolSite | |
| HET Code: | RFZ |
|---|---|
| Formula: | C12H12Cl2N2O4 |
| Molecular weight: | 319.141 g/mol |
| DrugBank ID: | DB08473 |
| Buried Surface Area: | 51.98 % |
| Polar Surface area: | 87.74 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -34.093 | -17.9416 | -31.9493 |
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 |
| C6 | CG2 | ILE- 10 | 3.68 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 10 | 4.44 | 0 | Hydrophobic |
| C1' | CG2 | ILE- 10 | 4.14 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 18 | 4.4 | 0 | Hydrophobic |
| CL1 | CB | ALA- 31 | 3.53 | 0 | Hydrophobic |
| C3 | CB | ALA- 31 | 3.91 | 0 | Hydrophobic |
| CL1 | CG2 | VAL- 64 | 4.49 | 0 | Hydrophobic |
| CL2 | CG | PHE- 80 | 4.03 | 0 | Hydrophobic |
| CL1 | CB | PHE- 80 | 4.22 | 0 | Hydrophobic |
| CL1 | CD1 | LEU- 83 | 4.33 | 0 | Hydrophobic |
| O2' | O | GLN- 131 | 3.23 | 140.71 | H-Bond (Ligand Donor) |
| C6 | CD2 | LEU- 134 | 4.02 | 0 | Hydrophobic |
| CL2 | CD1 | LEU- 134 | 4 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 134 | 3.3 | 0 | Hydrophobic |
| C5' | CB | ASP- 145 | 4.29 | 0 | Hydrophobic |
