sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2006-07-27
| 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: | 36.905 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.163 | 546.750 |
| % Hydrophobic | % Polar |
|---|---|
| 60.49 | 39.51 |
| According to VolSite | |
| HET Code: | 371 |
|---|---|
| Formula: | C19H16NO7S |
| Molecular weight: | 402.398 g/mol |
| DrugBank ID: | DB07024 |
| Buried Surface Area: | 68.6 % |
| Polar Surface area: | 135.58 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 27.047 | 28.8345 | 26.7461 |
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 |
| C16 | CG2 | ILE- 10 | 4.16 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 10 | 3.4 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 18 | 4.46 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 18 | 3.96 | 0 | Hydrophobic |
| C14 | CD | LYS- 33 | 3.87 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 64 | 4.03 | 0 | Hydrophobic |
| C11 | CB | PHE- 80 | 4.07 | 0 | Hydrophobic |
| O3 | O | GLU- 81 | 2.9 | 140.52 | H-Bond (Ligand Donor) |
| O2 | N | LEU- 83 | 2.9 | 170.8 | H-Bond (Protein Donor) |
| C17 | CB | GLN- 131 | 4.42 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 134 | 4.31 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 134 | 3.78 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 134 | 4.17 | 0 | Hydrophobic |
| C11 | CB | ALA- 144 | 3.68 | 0 | Hydrophobic |
| C13 | CB | ASP- 145 | 4.37 | 0 | Hydrophobic |
