sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2011-03-24
| 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: | 18.244 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.040 | 725.625 |
| % Hydrophobic | % Polar |
|---|---|
| 49.77 | 50.23 |
| According to VolSite | |
| HET Code: | Z46 |
|---|---|
| Formula: | C11H18N4O |
| Molecular weight: | 222.287 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.42 % |
| Polar Surface area: | 83.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -79.0907 | 135.64 | -63.2659 |
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 |
| C13 | CG1 | VAL- 18 | 4.13 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 18 | 4.21 | 0 | Hydrophobic |
| C10 | CB | ALA- 31 | 4.01 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 64 | 3.74 | 0 | Hydrophobic |
| C10 | CB | PHE- 80 | 3.7 | 0 | Hydrophobic |
| C11 | CD2 | PHE- 80 | 3.75 | 0 | Hydrophobic |
| N2 | O | GLU- 81 | 2.88 | 155.62 | H-Bond (Ligand Donor) |
| N1 | N | LEU- 83 | 3.21 | 169.44 | H-Bond (Protein Donor) |
| N7 | O | LEU- 83 | 2.67 | 128.12 | H-Bond (Ligand Donor) |
| C16 | CB | ASN- 132 | 3.35 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 134 | 3.69 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 134 | 4.3 | 0 | Hydrophobic |
| C12 | CB | ALA- 144 | 4.01 | 0 | Hydrophobic |
| C16 | CB | ALA- 144 | 4.24 | 0 | Hydrophobic |
| C11 | CB | ALA- 144 | 4.04 | 0 | Hydrophobic |
