sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2003-06-26
| 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: | 26.080 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.976 | 567.000 |
| % Hydrophobic | % Polar |
|---|---|
| 53.57 | 46.43 |
| According to VolSite | |
| HET Code: | N41 |
|---|---|
| Formula: | C19H22N6O2 |
| Molecular weight: | 366.417 g/mol |
| DrugBank ID: | DB08241 |
| Buried Surface Area: | 62.17 % |
| Polar Surface area: | 118.81 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 5.65596 | 43.9014 | 50.6636 |
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- 10 | 3.77 | 0 | Hydrophobic |
| C22 | CG2 | ILE- 10 | 3.52 | 0 | Hydrophobic |
| C10 | CB | VAL- 18 | 4.41 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 18 | 4.35 | 0 | Hydrophobic |
| N9 | O | GLU- 81 | 2.62 | 146.31 | H-Bond (Ligand Donor) |
| N3 | N | LEU- 83 | 3.25 | 161.06 | H-Bond (Protein Donor) |
| N25 | OD2 | ASP- 86 | 3.13 | 134.62 | H-Bond (Ligand Donor) |
| C14 | CG | GLN- 131 | 3.39 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 134 | 4.26 | 0 | Hydrophobic |
| C15 | CB | ASP- 145 | 4.09 | 0 | Hydrophobic |
