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
2000-09-20
| 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: | 36.824 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.127 | 475.875 |
| % Hydrophobic | % Polar |
|---|---|
| 58.87 | 41.13 |
| According to VolSite | |
| HET Code: | 106 |
|---|---|
| Formula: | C14H9BrN4O3S |
| Molecular weight: | 393.215 g/mol |
| DrugBank ID: | DB02973 |
| Buried Surface Area: | 60.77 % |
| Polar Surface area: | 122.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 38.4803 | 9.57765 | -11.6282 |
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 |
| C19 | CG2 | ILE- 10 | 3.45 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 18 | 4.04 | 0 | Hydrophobic |
| BR4 | CG2 | VAL- 18 | 4.16 | 0 | Hydrophobic |
| C7 | CB | ALA- 31 | 4.42 | 0 | Hydrophobic |
| C9 | CB | ALA- 31 | 4.03 | 0 | Hydrophobic |
| BR4 | CD | LYS- 33 | 4.21 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 64 | 3.53 | 0 | Hydrophobic |
| C7 | CG | PHE- 80 | 3.29 | 0 | Hydrophobic |
| N1 | O | GLU- 81 | 2.73 | 151.5 | H-Bond (Ligand Donor) |
| O11 | N | LEU- 83 | 2.76 | 163.18 | H-Bond (Protein Donor) |
| O28 | N | ASP- 86 | 3.1 | 153.4 | H-Bond (Protein Donor) |
| N30 | OD2 | ASP- 86 | 2.91 | 162.99 | H-Bond (Ligand Donor) |
| C23 | CB | ASP- 86 | 3.98 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 134 | 3.76 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 134 | 4.01 | 0 | Hydrophobic |
| C6 | CB | ALA- 144 | 4.04 | 0 | Hydrophobic |
| BR4 | CB | ASP- 145 | 4.34 | 0 | Hydrophobic |
