sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.990 Å
X-ray
2011-08-19
| 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: | 30.445 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.551 | 519.750 |
| % Hydrophobic | % Polar |
|---|---|
| 45.45 | 54.55 |
| According to VolSite | |
| HET Code: | B49 |
|---|---|
| Formula: | C22H28FN4O2 |
| Molecular weight: | 399.482 g/mol |
| DrugBank ID: | DB01268 |
| Buried Surface Area: | 58.71 % |
| Polar Surface area: | 78.43 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -91.5104 | -8.50297 | -83.0031 |
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 |
| C12 | CD1 | ILE- 10 | 4.04 | 0 | Hydrophobic |
| N25 | O | ILE- 10 | 2.84 | 155.26 | H-Bond (Ligand Donor) |
| C12 | CG1 | VAL- 18 | 4.18 | 0 | Hydrophobic |
| F29 | CG2 | VAL- 18 | 4.5 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 18 | 4.13 | 0 | Hydrophobic |
| C16 | CB | ALA- 31 | 3.6 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 64 | 3.49 | 0 | Hydrophobic |
| C16 | CB | PHE- 80 | 4.03 | 0 | Hydrophobic |
| F29 | CE2 | PHE- 80 | 4.42 | 0 | Hydrophobic |
| C6 | CG | PHE- 80 | 3.24 | 0 | Hydrophobic |
| N24 | O | GLU- 81 | 2.95 | 154.59 | H-Bond (Ligand Donor) |
| C4 | CZ | PHE- 82 | 3.81 | 0 | Hydrophobic |
| O27 | N | LEU- 83 | 2.94 | 169.66 | H-Bond (Protein Donor) |
| C3 | CB | ASP- 86 | 4.11 | 0 | Hydrophobic |
| O28 | N | ASP- 86 | 3.47 | 131.83 | H-Bond (Protein Donor) |
| N4 | OD2 | ASP- 86 | 2.56 | 144.33 | H-Bond (Ligand Donor) |
| N4 | OD2 | ASP- 86 | 2.56 | 0 | Ionic (Ligand Cationic) |
| N4 | OD1 | ASP- 86 | 3.75 | 0 | Ionic (Ligand Cationic) |
| C41 | CG | LYS- 88 | 3.52 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 134 | 4.01 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 134 | 3.51 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 134 | 3.57 | 0 | Hydrophobic |
| C5 | CB | ALA- 144 | 4.07 | 0 | Hydrophobic |
| C15 | CB | ASP- 145 | 3.79 | 0 | Hydrophobic |
