sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2011-02-15
| 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: | 22.117 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.143 | 681.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.44 | 43.56 |
| According to VolSite | |
| HET Code: | X06 |
|---|---|
| Formula: | C9H8ClN5O |
| Molecular weight: | 237.646 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.73 % |
| Polar Surface area: | 110.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -91.7206 | -8.90906 | -49.2494 |
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 |
| CL16 | CG2 | VAL- 18 | 4.16 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 18 | 3.79 | 0 | Hydrophobic |
| C08 | CB | ALA- 31 | 3.31 | 0 | Hydrophobic |
| C08 | CG1 | VAL- 64 | 4.08 | 0 | Hydrophobic |
| CL16 | CE2 | PHE- 80 | 3.83 | 0 | Hydrophobic |
| C07 | CB | PHE- 80 | 3.67 | 0 | Hydrophobic |
| N05 | O | LEU- 83 | 2.78 | 150.64 | H-Bond (Ligand Donor) |
| O15 | O | LEU- 83 | 3.08 | 126.58 | H-Bond (Ligand Donor) |
| O15 | N | LEU- 83 | 2.97 | 172.4 | H-Bond (Protein Donor) |
| N05 | O | HIS- 84 | 3.25 | 120.38 | H-Bond (Ligand Donor) |
| N04 | OD2 | ASP- 86 | 3.39 | 124.04 | H-Bond (Ligand Donor) |
| C09 | CD1 | LEU- 134 | 3.31 | 0 | Hydrophobic |
| C06 | CB | ALA- 144 | 3.98 | 0 | Hydrophobic |
| N02 | O | HOH- 405 | 2.93 | 166.46 | H-Bond (Protein Donor) |
