sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2005-11-08
| 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: | 27.686 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.590 | 671.625 |
| % Hydrophobic | % Polar |
|---|---|
| 44.72 | 55.28 |
| According to VolSite | |
| HET Code: | ZIP |
|---|---|
| Formula: | C10H13N5 |
| Molecular weight: | 203.244 g/mol |
| DrugBank ID: | DB08768 |
| Buried Surface Area: | 62.54 % |
| Polar Surface area: | 66.48 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 102.955 | 99.9617 | 80.4397 |
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 |
| C12 | CG2 | ILE- 10 | 3.92 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 18 | 3.39 | 0 | Hydrophobic |
| N9 | NZ | LYS- 33 | 3.1 | 137.21 | H-Bond (Protein Donor) |
| N7 | O | GLU- 81 | 2.8 | 163.52 | H-Bond (Ligand Donor) |
| N3 | N | LEU- 83 | 3.39 | 176.27 | H-Bond (Protein Donor) |
| C11 | CD2 | LEU- 134 | 4.17 | 0 | Hydrophobic |
