sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2006-08-21
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 62.916 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.107 | 556.875 |
| % Hydrophobic | % Polar |
|---|---|
| 48.48 | 51.52 |
| According to VolSite | |
| HET Code: | BLZ |
|---|---|
| Formula: | C22H20ClN3O4S |
| Molecular weight: | 457.930 g/mol |
| DrugBank ID: | DB07471 |
| Buried Surface Area: | 64.75 % |
| Polar Surface area: | 116.84 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -12.8074 | 206.044 | 112.847 |
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 |
| C28 | CD1 | ILE- 10 | 3.98 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 10 | 3.9 | 0 | Hydrophobic |
| C14 | CZ | TYR- 15 | 4.08 | 0 | Hydrophobic |
| CL2 | CG2 | VAL- 18 | 3.78 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 18 | 3.68 | 0 | Hydrophobic |
| C27 | CB | ALA- 31 | 4.31 | 0 | Hydrophobic |
| C14 | CD | LYS- 33 | 3.99 | 0 | Hydrophobic |
| N26 | OE2 | GLU- 51 | 2.89 | 141.89 | H-Bond (Ligand Donor) |
| S23 | CG1 | VAL- 64 | 3.99 | 0 | Hydrophobic |
| S23 | CB | PHE- 80 | 4.27 | 0 | Hydrophobic |
| C1 | CZ | PHE- 82 | 3.69 | 0 | Hydrophobic |
| N6 | N | LEU- 83 | 2.96 | 172.87 | H-Bond (Protein Donor) |
| S23 | CD1 | LEU- 134 | 3.75 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 134 | 3.71 | 0 | Hydrophobic |
| S23 | CB | ALA- 144 | 4.09 | 0 | Hydrophobic |
| O25 | N | ASP- 145 | 3.02 | 163.92 | H-Bond (Protein Donor) |
| C16 | CB | ASP- 145 | 3.68 | 0 | Hydrophobic |
