sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2010-12-10
| 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: | 25.883 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.606 | 621.000 |
| % Hydrophobic | % Polar |
|---|---|
| 42.39 | 57.61 |
| According to VolSite | |
| HET Code: | SU9 |
|---|---|
| Formula: | C13H11N3O2 |
| Molecular weight: | 241.245 g/mol |
| DrugBank ID: | DB03428 |
| Buried Surface Area: | 69.56 % |
| Polar Surface area: | 67.01 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -92.7794 | 80.2952 | 85.2746 |
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 |
| C2 | CG2 | VAL- 18 | 4.24 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 18 | 4.4 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 18 | 4.16 | 0 | Hydrophobic |
| C6 | CB | ALA- 31 | 3.91 | 0 | Hydrophobic |
| C4 | CB | ALA- 31 | 4.12 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 64 | 4 | 0 | Hydrophobic |
| C6 | CB | PHE- 80 | 3.41 | 0 | Hydrophobic |
| N7 | O | GLU- 81 | 3.06 | 177.26 | H-Bond (Ligand Donor) |
| O10 | N | LEU- 83 | 2.79 | 167.17 | H-Bond (Protein Donor) |
| C6 | CD1 | LEU- 134 | 4.15 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 134 | 3.52 | 0 | Hydrophobic |
| C1 | CB | ALA- 144 | 3.88 | 0 | Hydrophobic |
| C12 | CB | ASP- 145 | 3.94 | 0 | Hydrophobic |
