sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2012-05-02
| 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: | 24.737 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.063 | 570.375 |
| % Hydrophobic | % Polar |
|---|---|
| 53.85 | 46.15 |
| According to VolSite | |
| HET Code: | 0S0 |
|---|---|
| Formula: | C11H9N4O4S |
| Molecular weight: | 293.279 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.85 % |
| Polar Surface area: | 145.41 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -2.98465 | -7.143 | 27.9338 |
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 | 3.36 | 0 | Hydrophobic |
| N03 | O | GLU- 81 | 3 | 172.3 | H-Bond (Ligand Donor) |
| O01 | N | LEU- 83 | 3.04 | 165.36 | H-Bond (Protein Donor) |
| N10 | O | LEU- 83 | 3.45 | 120.87 | H-Bond (Ligand Donor) |
| O18 | N | ASP- 86 | 3.03 | 162.96 | H-Bond (Protein Donor) |
| C13 | CB | ASP- 86 | 4.01 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 134 | 4.19 | 0 | Hydrophobic |
