sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.880 Å
X-ray
2005-09-27
| 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: | 43.895 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.981 | 793.125 |
| % Hydrophobic | % Polar |
|---|---|
| 48.94 | 51.06 |
| According to VolSite | |
| HET Code: | D42 |
|---|---|
| Formula: | C21H24N7O2S |
| Molecular weight: | 438.526 g/mol |
| DrugBank ID: | DB07622 |
| Buried Surface Area: | 64.28 % |
| Polar Surface area: | 135.69 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 80.5396 | 61.5539 | 12.619 |
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 |
| S38 | CG2 | ILE- 10 | 3.82 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 18 | 4.03 | 0 | Hydrophobic |
| C26 | CB | ALA- 31 | 3.47 | 0 | Hydrophobic |
| C25 | CG1 | VAL- 64 | 3.67 | 0 | Hydrophobic |
| C24 | CB | PHE- 80 | 3.5 | 0 | Hydrophobic |
| C42 | CE2 | PHE- 82 | 3.37 | 0 | Hydrophobic |
| N34 | N | LEU- 83 | 2.9 | 149.81 | H-Bond (Protein Donor) |
| S38 | CB | ASP- 86 | 4.16 | 0 | Hydrophobic |
| C46 | CG | LYS- 89 | 3.72 | 0 | Hydrophobic |
| C26 | CD1 | LEU- 134 | 3.31 | 0 | Hydrophobic |
| C23 | CB | ALA- 144 | 4.13 | 0 | Hydrophobic |
| C2 | CB | ASP- 145 | 3.78 | 0 | Hydrophobic |
