sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.720 Å
X-ray
2007-04-27
| 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: | 20.446 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.906 | 610.875 |
| % Hydrophobic | % Polar |
|---|---|
| 44.20 | 55.80 |
| According to VolSite | |
| HET Code: | C85 |
|---|---|
| Formula: | C14H12N3O4S2 |
| Molecular weight: | 350.393 g/mol |
| DrugBank ID: | DB07534 |
| Buried Surface Area: | 57.95 % |
| Polar Surface area: | 161.66 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 91.0162 | 71.8768 | 13.8838 |
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 | CD1 | ILE- 10 | 4.03 | 0 | Hydrophobic |
| S1 | CG2 | VAL- 18 | 4.34 | 0 | Hydrophobic |
| C6 | CB | ALA- 31 | 3.72 | 0 | Hydrophobic |
| C6 | CB | PHE- 80 | 4.45 | 0 | Hydrophobic |
| C15 | CB | GLN- 85 | 4.43 | 0 | Hydrophobic |
| O3 | N | ASP- 86 | 2.81 | 170.49 | H-Bond (Protein Donor) |
| N6 | OD2 | ASP- 86 | 3.07 | 144.39 | H-Bond (Ligand Donor) |
| C17 | CB | ASP- 86 | 3.93 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 134 | 3.95 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 134 | 3.52 | 0 | Hydrophobic |
| N2 | N | ASP- 145 | 3.41 | 130.29 | H-Bond (Protein Donor) |
