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
2007-04-27
| 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 |
|---|---|
| C | 100 % |
| B-Factor: | 33.112 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.687 | 516.375 |
| % Hydrophobic | % Polar |
|---|---|
| 47.71 | 52.29 |
| According to VolSite | |
| HET Code: | C95 |
|---|---|
| Formula: | C15H10N2O4S |
| Molecular weight: | 314.316 g/mol |
| DrugBank ID: | DB07539 |
| Buried Surface Area: | 65.94 % |
| Polar Surface area: | 133.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -13.0141 | -16.0461 | 40.164 |
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 |
| C14 | CD1 | ILE- 10 | 3.59 | 0 | Hydrophobic |
| S1 | CG2 | VAL- 18 | 4.14 | 0 | Hydrophobic |
| O3 | NZ | LYS- 89 | 3.19 | 160.96 | H-Bond (Protein Donor) |
| O3 | NZ | LYS- 89 | 3.19 | 0 | Ionic (Protein Cationic) |
| C18 | CD2 | LEU- 134 | 3.66 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 145 | 2.95 | 172.48 | H-Bond (Ligand Donor) |
