sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.550 Å
X-ray
2007-08-29
| 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: | 23.603 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.339 | 529.875 |
| % Hydrophobic | % Polar |
|---|---|
| 39.49 | 60.51 |
| According to VolSite | |
| HET Code: | SC9 |
|---|---|
| Formula: | C18H14FN5 |
| Molecular weight: | 319.336 g/mol |
| DrugBank ID: | DB08532 |
| Buried Surface Area: | 66.83 % |
| Polar Surface area: | 55.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 1.61546 | 27.0336 | 8.23142 |
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 | 4.34 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 18 | 4.37 | 0 | Hydrophobic |
| C20 | CB | ALA- 31 | 3.29 | 0 | Hydrophobic |
| C20 | CB | ALA- 31 | 3.29 | 0 | Hydrophobic |
| C22 | CD | LYS- 33 | 4.31 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 64 | 4.07 | 0 | Hydrophobic |
| C21 | CB | PHE- 80 | 3.83 | 0 | Hydrophobic |
| F24 | CD1 | PHE- 82 | 3.69 | 0 | Hydrophobic |
| C11 | CB | ASP- 86 | 3.71 | 0 | Hydrophobic |
| N04 | NZ | LYS- 89 | 3.21 | 146.01 | H-Bond (Protein Donor) |
| C11 | CD2 | LEU- 134 | 4.22 | 0 | Hydrophobic |
| F24 | CD1 | LEU- 134 | 3.58 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 134 | 3.28 | 0 | Hydrophobic |
| C22 | CB | ALA- 144 | 4.17 | 0 | Hydrophobic |
| N04 | O | HOH- 1216 | 2.56 | 155.9 | H-Bond (Protein Donor) |
