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
2011-04-17
| 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: | 26.774 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.907 | 1660.500 |
| % Hydrophobic | % Polar |
|---|---|
| 45.53 | 54.47 |
| According to VolSite | |
| HET Code: | 12Z |
|---|---|
| Formula: | C15H18N4OS |
| Molecular weight: | 302.395 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.73 % |
| Polar Surface area: | 109.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -92.89 | -44.8556 | -48.1561 |
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 |
| S5 | CG2 | ILE- 10 | 3.36 | 0 | Hydrophobic |
| C18 | CG2 | ILE- 10 | 3.63 | 0 | Hydrophobic |
| C19 | CG1 | ILE- 10 | 4.07 | 0 | Hydrophobic |
| S5 | CG1 | VAL- 18 | 4.48 | 0 | Hydrophobic |
| N7 | O | GLU- 81 | 2.7 | 146.74 | H-Bond (Ligand Donor) |
| C18 | CE2 | PHE- 82 | 4.22 | 0 | Hydrophobic |
| C19 | CZ | PHE- 82 | 3.67 | 0 | Hydrophobic |
| N3 | N | LEU- 83 | 3.45 | 174.04 | H-Bond (Protein Donor) |
| N8 | O | LEU- 83 | 2.87 | 141.71 | H-Bond (Ligand Donor) |
| C16 | CB | ASP- 86 | 4.21 | 0 | Hydrophobic |
| C21 | CD | LYS- 89 | 3.97 | 0 | Hydrophobic |
| S5 | CD1 | LEU- 134 | 4.13 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 134 | 4.42 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 134 | 4.22 | 0 | Hydrophobic |
| C14 | CB | ALA- 144 | 4.29 | 0 | Hydrophobic |
| C15 | CB | ASP- 145 | 4.02 | 0 | Hydrophobic |
