sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2011-03-24
| 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: | 31.094 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.924 | 769.500 |
| % Hydrophobic | % Polar |
|---|---|
| 43.42 | 56.58 |
| According to VolSite | |
| HET Code: | Z30 |
|---|---|
| Formula: | C12H20N4O |
| Molecular weight: | 236.313 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.54 % |
| Polar Surface area: | 83.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 105.617 | 136.525 | 98.3569 |
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 | 4.17 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 18 | 3.75 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 18 | 4.05 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 18 | 4.38 | 0 | Hydrophobic |
| C11 | CB | ALA- 31 | 4.3 | 0 | Hydrophobic |
| C4 | CB | ALA- 31 | 3.66 | 0 | Hydrophobic |
| C10 | CD | LYS- 33 | 4.16 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 64 | 3.81 | 0 | Hydrophobic |
| C4 | CB | PHE- 80 | 3.32 | 0 | Hydrophobic |
| C5 | CD2 | PHE- 80 | 3.68 | 0 | Hydrophobic |
| C10 | CE2 | PHE- 80 | 4.45 | 0 | Hydrophobic |
| N2 | O | GLU- 81 | 2.81 | 154.59 | H-Bond (Ligand Donor) |
| N1 | N | LEU- 83 | 2.83 | 166.34 | H-Bond (Protein Donor) |
| C4 | CD1 | LEU- 134 | 3.72 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 134 | 4.15 | 0 | Hydrophobic |
| C6 | CB | ALA- 144 | 4.41 | 0 | Hydrophobic |
| C8 | CB | ALA- 144 | 4.47 | 0 | Hydrophobic |
| C5 | CB | ALA- 144 | 4.37 | 0 | Hydrophobic |
