sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2001-11-14
| 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: | 30.064 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.910 | 563.625 |
| % Hydrophobic | % Polar |
|---|---|
| 50.30 | 49.70 |
| According to VolSite | |
| HET Code: | LS5 |
|---|---|
| Formula: | C16H15N5O3S |
| Molecular weight: | 357.387 g/mol |
| DrugBank ID: | DB08126 |
| Buried Surface Area: | 55.14 % |
| Polar Surface area: | 145.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -10.1053 | 48.4429 | 10.822 |
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 |
| C25 | CG2 | ILE- 10 | 3.51 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 18 | 4.12 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 18 | 4.07 | 0 | Hydrophobic |
| C7 | CB | ALA- 31 | 4.27 | 0 | Hydrophobic |
| C9 | CB | ALA- 31 | 4.14 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 64 | 3.91 | 0 | Hydrophobic |
| C7 | CG | PHE- 80 | 3.46 | 0 | Hydrophobic |
| N1 | O | GLU- 81 | 2.94 | 155.81 | H-Bond (Ligand Donor) |
| O11 | N | LEU- 83 | 2.98 | 165.75 | H-Bond (Protein Donor) |
| O32 | N | ASP- 86 | 3.41 | 142.81 | H-Bond (Protein Donor) |
| C24 | CB | ASP- 86 | 4.06 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 134 | 3.96 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 134 | 3.89 | 0 | Hydrophobic |
| C6 | CB | ALA- 144 | 3.92 | 0 | Hydrophobic |
