sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2003-10-20
| 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: | 18.510 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.912 | 489.375 |
| % Hydrophobic | % Polar |
|---|---|
| 51.72 | 48.28 |
| According to VolSite | |
| HET Code: | FMD |
|---|---|
| Formula: | C20H21FN3O4 |
| Molecular weight: | 386.397 g/mol |
| DrugBank ID: | DB03737 |
| Buried Surface Area: | 70.45 % |
| Polar Surface area: | 122.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 13.1287 | -8.19904 | 11.0744 |
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 |
| C11 | CG2 | ILE- 10 | 3.99 | 0 | Hydrophobic |
| C22 | CG2 | ILE- 10 | 3.55 | 0 | Hydrophobic |
| F17 | CG2 | VAL- 18 | 4.22 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 18 | 4.25 | 0 | Hydrophobic |
| F17 | CE | LYS- 33 | 4.16 | 0 | Hydrophobic |
| O10 | N | LEU- 83 | 2.78 | 175.6 | H-Bond (Protein Donor) |
| C22 | CB | ASP- 86 | 4.33 | 0 | Hydrophobic |
| C25 | CB | GLN- 131 | 3.86 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 134 | 3.54 | 0 | Hydrophobic |
| F17 | CB | ASP- 145 | 3.24 | 0 | Hydrophobic |
| C18 | CB | ASP- 145 | 4.25 | 0 | Hydrophobic |
| O27 | OD2 | ASP- 145 | 2.77 | 169.14 | H-Bond (Ligand Donor) |
