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
2002-06-27
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 32.730 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.735 | 610.875 |
| % Hydrophobic | % Polar |
|---|---|
| 46.96 | 53.04 |
| According to VolSite | |
| HET Code: | 207 |
|---|---|
| Formula: | C13H18N4O |
| Molecular weight: | 246.308 g/mol |
| DrugBank ID: | DB02603 |
| Buried Surface Area: | 61.28 % |
| Polar Surface area: | 76.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 1.11622 | 28.6549 | 9.12244 |
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 |
| C12 | CG2 | ILE- 10 | 3.4 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 18 | 3.92 | 0 | Hydrophobic |
| C4 | CB | ALA- 31 | 3.65 | 0 | Hydrophobic |
| N9 | O | GLU- 81 | 2.92 | 167.69 | H-Bond (Ligand Donor) |
| C3 | CB | LEU- 83 | 4.46 | 0 | Hydrophobic |
| C14 | CB | GLN- 131 | 3.83 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 134 | 3.33 | 0 | Hydrophobic |
