sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.210 Å
X-ray
2004-05-07
| 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: | 40.681 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.816 | 499.500 |
| % Hydrophobic | % Polar |
|---|---|
| 51.35 | 48.65 |
| According to VolSite | |
| HET Code: | N5B |
|---|---|
| Formula: | C13H13N3O |
| Molecular weight: | 227.262 g/mol |
| DrugBank ID: | DB02647 |
| Buried Surface Area: | 60.98 % |
| Polar Surface area: | 57.78 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 10.9961 | 46.6099 | 24.4641 |
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 |
| C11 | CG2 | ILE- 10 | 3.7 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 18 | 3.79 | 0 | Hydrophobic |
| C5 | CB | ALA- 31 | 3.75 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 64 | 4.21 | 0 | Hydrophobic |
| C2 | CB | PHE- 80 | 3.76 | 0 | Hydrophobic |
| C5 | CD1 | PHE- 80 | 3.77 | 0 | Hydrophobic |
| N4 | O | GLU- 81 | 2.66 | 155.32 | H-Bond (Ligand Donor) |
| N8 | N | LEU- 83 | 2.88 | 161.61 | H-Bond (Protein Donor) |
| N9 | O | LEU- 83 | 2.98 | 125.67 | H-Bond (Ligand Donor) |
| C13 | CB | ASP- 86 | 4.33 | 0 | Hydrophobic |
| C15 | CD | LYS- 89 | 4.36 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 134 | 4.06 | 0 | Hydrophobic |
| C6 | CB | ALA- 144 | 3.78 | 0 | Hydrophobic |
