sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2001-11-14
| 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: | 34.600 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.791 | 509.625 |
| % Hydrophobic | % Polar |
|---|---|
| 50.99 | 49.01 |
| According to VolSite | |
| HET Code: | LS4 |
|---|---|
| Formula: | C18H14N4O3S2 |
| Molecular weight: | 398.459 g/mol |
| DrugBank ID: | DB08125 |
| Buried Surface Area: | 62.29 % |
| Polar Surface area: | 136.81 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -10.2632 | 47.904 | 10.6746 |
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 |
| C17 | CG2 | ILE- 10 | 3.47 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 18 | 4.21 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 18 | 4.06 | 0 | Hydrophobic |
| C13 | CB | ALA- 31 | 4.23 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 64 | 4.02 | 0 | Hydrophobic |
| C9 | CB | PHE- 80 | 3.55 | 0 | Hydrophobic |
| N7 | O | GLU- 81 | 3.06 | 149.55 | H-Bond (Ligand Donor) |
| O5 | N | LEU- 83 | 2.98 | 165.61 | H-Bond (Protein Donor) |
| N16 | O | LEU- 83 | 3.41 | 137.28 | H-Bond (Ligand Donor) |
| C19 | CB | ASP- 86 | 3.82 | 0 | Hydrophobic |
| O24 | NZ | LYS- 89 | 3.28 | 135.31 | H-Bond (Protein Donor) |
| C13 | CD1 | LEU- 134 | 3.85 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 134 | 3.78 | 0 | Hydrophobic |
| C10 | CB | ALA- 144 | 4.03 | 0 | Hydrophobic |
