sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2004-05-07
| 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: | 51.355 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.588 | 573.750 |
| % Hydrophobic | % Polar |
|---|---|
| 42.35 | 57.65 |
| According to VolSite | |
| HET Code: | 292 |
|---|---|
| Formula: | C18H17N3O |
| Molecular weight: | 291.347 g/mol |
| DrugBank ID: | DB06944 |
| Buried Surface Area: | 56.11 % |
| Polar Surface area: | 57.78 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -36.3438 | 169.52 | 87.8052 |
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 |
| C20 | CG | GLU- 8 | 4.07 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 10 | 3.94 | 0 | Hydrophobic |
| C17 | CG2 | ILE- 10 | 3.53 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 18 | 4.21 | 0 | Hydrophobic |
| C3 | CB | ALA- 31 | 3.62 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 64 | 4.28 | 0 | Hydrophobic |
| C1 | CD1 | PHE- 80 | 4.05 | 0 | Hydrophobic |
| C2 | CG | PHE- 80 | 4.1 | 0 | Hydrophobic |
| C3 | CB | PHE- 80 | 3.64 | 0 | Hydrophobic |
| N8 | O | GLU- 81 | 2.77 | 155.4 | H-Bond (Ligand Donor) |
| N7 | N | LEU- 83 | 2.89 | 166.71 | H-Bond (Protein Donor) |
| N9 | O | LEU- 83 | 2.84 | 172.47 | H-Bond (Ligand Donor) |
| C11 | CD2 | LEU- 134 | 4.29 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 134 | 4.22 | 0 | Hydrophobic |
