sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.490 Å
X-ray
2012-05-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.430 | 4.430 | 4.430 | 0.000 | 4.430 | 1 |
| 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: | 53.876 |
|---|---|
| Number of residues: | 17 |
| Including | |
| Standard Amino Acids: | 16 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.328 | 1485.000 |
| % Hydrophobic | % Polar |
|---|---|
| 64.09 | 35.91 |
| According to VolSite | |
| HET Code: | 2AN |
|---|---|
| Formula: | C16H12NO3S |
| Molecular weight: | 298.336 g/mol |
| DrugBank ID: | DB04474 |
| Buried Surface Area: | 38.31 % |
| Polar Surface area: | 77.61 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 16.719 | 4.22157 | -29.6004 |
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 |
| C15 | CD2 | LEU- 37 | 3.91 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 49 | 4.02 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 52 | 3.46 | 0 | Hydrophobic |
| C10 | CG2 | ILE- 52 | 3.86 | 0 | Hydrophobic |
| C8 | CD | LYS- 56 | 3.94 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 69 | 3.69 | 0 | Hydrophobic |
| O1 | NE2 | HIS- 71 | 3.08 | 126.6 | H-Bond (Protein Donor) |
| C16 | CD1 | LEU- 76 | 3.71 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 76 | 3.41 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 76 | 3.41 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 78 | 3.66 | 0 | Hydrophobic |
