sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2011-03-24
| 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: | 24.075 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.185 | 573.750 |
| % Hydrophobic | % Polar |
|---|---|
| 58.82 | 41.18 |
| According to VolSite | |
| HET Code: | Z63 |
|---|---|
| Formula: | C12H12N4OS |
| Molecular weight: | 260.315 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.69 % |
| Polar Surface area: | 109.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -66.1036 | -44.6751 | -47.3225 |
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 |
| S13 | CD1 | ILE- 10 | 4.01 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 10 | 3.73 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 18 | 4.34 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 18 | 3.92 | 0 | Hydrophobic |
| S13 | CB | ALA- 31 | 4.35 | 0 | Hydrophobic |
| N3 | O | GLU- 81 | 2.59 | 137.5 | H-Bond (Ligand Donor) |
| C16 | CE2 | PHE- 82 | 4.04 | 0 | Hydrophobic |
| N1 | N | LEU- 83 | 3.22 | 175.47 | H-Bond (Protein Donor) |
| N15 | O | LEU- 83 | 2.72 | 139.24 | H-Bond (Ligand Donor) |
| C18 | CB | ASP- 86 | 3.62 | 0 | Hydrophobic |
| S13 | CD1 | LEU- 134 | 4.08 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 134 | 3.57 | 0 | Hydrophobic |
| C6 | CB | ALA- 144 | 4.47 | 0 | Hydrophobic |
| C11 | CB | ASP- 145 | 4.22 | 0 | Hydrophobic |
