sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2011-03-14
| 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: | 29.476 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.898 | 597.375 |
| % Hydrophobic | % Polar |
|---|---|
| 45.20 | 54.80 |
| According to VolSite | |
| HET Code: | XA0 |
|---|---|
| Formula: | C14H9ClF3N3O3 |
| Molecular weight: | 359.688 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.14 % |
| Polar Surface area: | 100.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -65.3323 | -10.5575 | 25.4584 |
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 |
| CL21 | CG2 | ILE- 10 | 3.76 | 0 | Hydrophobic |
| F22 | CG1 | ILE- 10 | 4.07 | 0 | Hydrophobic |
| C06 | CD1 | ILE- 10 | 4.12 | 0 | Hydrophobic |
| C07 | CG2 | ILE- 10 | 3.47 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 10 | 3.78 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 10 | 3.64 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 10 | 3.64 | 0 | Hydrophobic |
| C04 | CG1 | VAL- 18 | 4.24 | 0 | Hydrophobic |
| C08 | CG1 | VAL- 18 | 3.9 | 0 | Hydrophobic |
| CL21 | CG2 | VAL- 18 | 3.95 | 0 | Hydrophobic |
| F22 | CD | LYS- 20 | 4.37 | 0 | Hydrophobic |
| C04 | CB | ALA- 31 | 3.62 | 0 | Hydrophobic |
| N02 | O | GLU- 81 | 2.97 | 156.1 | H-Bond (Ligand Donor) |
| F22 | CZ | PHE- 82 | 3.4 | 0 | Hydrophobic |
| N01 | O | LEU- 83 | 2.98 | 127.56 | H-Bond (Ligand Donor) |
| O18 | N | LEU- 83 | 2.88 | 173.67 | H-Bond (Protein Donor) |
| C11 | CD2 | LEU- 134 | 4.05 | 0 | Hydrophobic |
| C05 | CD1 | LEU- 134 | 3.61 | 0 | Hydrophobic |
