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
2001-02-06
| 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: | 31.601 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.918 | 475.875 |
| % Hydrophobic | % Polar |
|---|---|
| 49.65 | 50.35 |
| According to VolSite | |
| HET Code: | 2PU |
|---|---|
| Formula: | C19H23N6O2 |
| Molecular weight: | 367.425 g/mol |
| DrugBank ID: | DB06976 |
| Buried Surface Area: | 63.64 % |
| Polar Surface area: | 106.72 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 6.73519 | 9.44515 | 25.48 |
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 |
| C6 | CG2 | ILE- 10 | 3.56 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 18 | 4.31 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 18 | 4.22 | 0 | Hydrophobic |
| C9 | CB | ALA- 31 | 3.37 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 64 | 4.1 | 0 | Hydrophobic |
| C14 | CB | PHE- 80 | 3.59 | 0 | Hydrophobic |
| N16 | O | VAL- 83 | 2.62 | 171.67 | H-Bond (Ligand Donor) |
| O17 | N | VAL- 83 | 2.69 | 148.74 | H-Bond (Protein Donor) |
| N25 | OD2 | ASP- 86 | 2.82 | 149.5 | H-Bond (Ligand Donor) |
| N25 | OD2 | ASP- 86 | 2.82 | 0 | Ionic (Ligand Cationic) |
| C1 | CD1 | LEU- 134 | 4.1 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 134 | 3.57 | 0 | Hydrophobic |
| C3 | CB | ALA- 144 | 3.95 | 0 | Hydrophobic |
