sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2005-09-27
| 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: | 32.421 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.038 | 597.375 |
| % Hydrophobic | % Polar |
|---|---|
| 53.11 | 46.89 |
| According to VolSite | |
| HET Code: | D31 |
|---|---|
| Formula: | C24H33N5O2 |
| Molecular weight: | 423.551 g/mol |
| DrugBank ID: | DB07618 |
| Buried Surface Area: | 66.88 % |
| Polar Surface area: | 106.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 27.4724 | 10.4607 | 12.7681 |
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 |
| C36 | CG2 | ILE- 10 | 3.62 | 0 | Hydrophobic |
| C30 | CG1 | VAL- 18 | 4.12 | 0 | Hydrophobic |
| C29 | CB | ALA- 31 | 3.56 | 0 | Hydrophobic |
| O53 | NZ | LYS- 33 | 3.46 | 130.03 | H-Bond (Protein Donor) |
| C28 | CG1 | VAL- 64 | 3.73 | 0 | Hydrophobic |
| C27 | CB | PHE- 80 | 3.57 | 0 | Hydrophobic |
| C36 | CE1 | PHE- 82 | 4.45 | 0 | Hydrophobic |
| C37 | CZ | PHE- 82 | 3.9 | 0 | Hydrophobic |
| N34 | O | LEU- 83 | 2.64 | 158.99 | H-Bond (Ligand Donor) |
| N55 | N | LEU- 83 | 3.04 | 176.3 | H-Bond (Protein Donor) |
| N1 | OD2 | ASP- 86 | 3.06 | 0 | Ionic (Ligand Cationic) |
| C41 | CB | ASP- 86 | 4.18 | 0 | Hydrophobic |
| C39 | CD | LYS- 89 | 3.62 | 0 | Hydrophobic |
| N1 | O | GLN- 131 | 3.41 | 168.87 | H-Bond (Ligand Donor) |
| C10 | CB | GLN- 131 | 3.85 | 0 | Hydrophobic |
| C41 | CD2 | LEU- 134 | 4.11 | 0 | Hydrophobic |
| C29 | CD1 | LEU- 134 | 3.55 | 0 | Hydrophobic |
| C27 | CB | ALA- 144 | 4.34 | 0 | Hydrophobic |
