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
2010-01-18
| 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: | 25.677 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.877 | 820.125 |
| % Hydrophobic | % Polar |
|---|---|
| 43.21 | 56.79 |
| According to VolSite | |
| HET Code: | A07 |
|---|---|
| Formula: | C17H16ClN3O |
| Molecular weight: | 313.781 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.03 % |
| Polar Surface area: | 57.78 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 41.2125 | -9.39923 | 25.0762 |
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 | CD1 | ILE- 10 | 3.81 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 18 | 4.4 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 18 | 3.62 | 0 | Hydrophobic |
| C14 | CB | ALA- 31 | 3.58 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 64 | 4.08 | 0 | Hydrophobic |
| CL1 | CE2 | PHE- 80 | 3.64 | 0 | Hydrophobic |
| C13 | CB | PHE- 80 | 3.9 | 0 | Hydrophobic |
| N20 | O | GLU- 81 | 2.95 | 172.63 | H-Bond (Ligand Donor) |
| N21 | N | LEU- 83 | 3.31 | 163.61 | H-Bond (Protein Donor) |
| N23 | O | LEU- 83 | 3.18 | 133.37 | H-Bond (Ligand Donor) |
| C29 | CB | ASP- 86 | 3.59 | 0 | Hydrophobic |
| C3 | CB | ASN- 132 | 3.77 | 0 | Hydrophobic |
| C29 | CD2 | LEU- 134 | 3.98 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 134 | 3.43 | 0 | Hydrophobic |
| CL1 | CB | ALA- 144 | 3.74 | 0 | Hydrophobic |
| C2 | CB | ALA- 144 | 4.02 | 0 | Hydrophobic |
