sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2012-10-02
| 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: | 30.369 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.795 | 573.750 |
| % Hydrophobic | % Polar |
|---|---|
| 51.18 | 48.82 |
| According to VolSite | |
| HET Code: | T9N |
|---|---|
| Formula: | C16H14N6OS |
| Molecular weight: | 338.387 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.23 % |
| Polar Surface area: | 134.99 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 6.55683 | 23.021 | 23.0128 |
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 |
| C13 | CG2 | ILE- 10 | 3.41 | 0 | Hydrophobic |
| C06 | CG1 | VAL- 18 | 3.69 | 0 | Hydrophobic |
| C06 | CB | ALA- 31 | 4.32 | 0 | Hydrophobic |
| C21 | CB | ALA- 31 | 3.9 | 0 | Hydrophobic |
| C06 | CD | LYS- 33 | 4.4 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 64 | 4.48 | 0 | Hydrophobic |
| C06 | CD2 | PHE- 80 | 3.41 | 0 | Hydrophobic |
| C21 | CB | PHE- 80 | 4.43 | 0 | Hydrophobic |
| N19 | N | LEU- 83 | 3.02 | 170.17 | H-Bond (Protein Donor) |
| O15 | OD2 | ASP- 86 | 2.61 | 132.58 | H-Bond (Ligand Donor) |
| C14 | CB | ASP- 86 | 4.02 | 0 | Hydrophobic |
| C16 | CD | LYS- 89 | 3.88 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 134 | 3.24 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 134 | 4.17 | 0 | Hydrophobic |
| C01 | CB | ASP- 145 | 3.86 | 0 | Hydrophobic |
