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
2011-02-23
| 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: | 27.278 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.718 | 502.875 |
| % Hydrophobic | % Polar |
|---|---|
| 42.95 | 57.05 |
| According to VolSite | |
| HET Code: | X35 |
|---|---|
| Formula: | C12H12N4OS |
| Molecular weight: | 260.315 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.51 % |
| Polar Surface area: | 109.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -66.5733 | -80.0458 | -84.3126 |
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 |
| S13 | CD1 | ILE- 10 | 3.86 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 10 | 3.62 | 0 | Hydrophobic |
| S13 | CG1 | VAL- 18 | 4.48 | 0 | Hydrophobic |
| S13 | CB | ALA- 31 | 4.49 | 0 | Hydrophobic |
| N8 | NZ | LYS- 33 | 3.02 | 175.38 | H-Bond (Protein Donor) |
| N3 | O | GLU- 81 | 2.71 | 146.91 | H-Bond (Ligand Donor) |
| C16 | CE2 | PHE- 82 | 4 | 0 | Hydrophobic |
| N1 | N | LEU- 83 | 3.32 | 168.06 | H-Bond (Protein Donor) |
| N15 | O | LEU- 83 | 2.8 | 137.47 | H-Bond (Ligand Donor) |
| C18 | CB | ASP- 86 | 3.66 | 0 | Hydrophobic |
| S13 | CD1 | LEU- 134 | 4.05 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 134 | 3.86 | 0 | Hydrophobic |
| C6 | CB | ALA- 144 | 4.34 | 0 | Hydrophobic |
| C10 | CB | ASP- 145 | 3.87 | 0 | Hydrophobic |
