sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2002-07-21
| 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 |
|---|---|
| C | 100 % |
| B-Factor: | 55.549 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.612 | 482.625 |
| % Hydrophobic | % Polar |
|---|---|
| 51.75 | 48.25 |
| According to VolSite | |
| HET Code: | 2A6 |
|---|---|
| Formula: | C18H21N5O |
| Molecular weight: | 323.392 g/mol |
| DrugBank ID: | DB06948 |
| Buried Surface Area: | 65.76 % |
| Polar Surface area: | 75.72 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 34.5718 | 83.9633 | 42.9643 |
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 |
| C10 | CG2 | ILE- 10 | 3.84 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 10 | 4.47 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 10 | 4.11 | 0 | Hydrophobic |
| C21 | CG2 | ILE- 10 | 4.15 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 18 | 3.93 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 18 | 4.34 | 0 | Hydrophobic |
| N9 | O | GLU- 81 | 2.82 | 154.57 | H-Bond (Ligand Donor) |
| N3 | N | LEU- 83 | 3.19 | 177.65 | H-Bond (Protein Donor) |
| N2 | O | LEU- 83 | 2.66 | 140.96 | H-Bond (Ligand Donor) |
| C20 | CB | GLN- 85 | 4.05 | 0 | Hydrophobic |
| C21 | CB | ASP- 86 | 4.46 | 0 | Hydrophobic |
| C20 | CD | LYS- 89 | 4.14 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 134 | 4.36 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 134 | 4.33 | 0 | Hydrophobic |
| C15 | CB | ASP- 145 | 4.26 | 0 | Hydrophobic |
