sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2007-08-29
| 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: | 34.441 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.441 | 664.875 |
| % Hydrophobic | % Polar |
|---|---|
| 40.10 | 59.90 |
| According to VolSite | |
| HET Code: | SCX |
|---|---|
| Formula: | C19H17F2N7 |
| Molecular weight: | 381.382 g/mol |
| DrugBank ID: | DB08538 |
| Buried Surface Area: | 71.1 % |
| Polar Surface area: | 94.02 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 1.27404 | 27.6235 | 8.56193 |
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 |
| F28 | CG1 | ILE- 10 | 3.9 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 18 | 3.99 | 0 | Hydrophobic |
| F28 | CB | VAL- 18 | 3.53 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 18 | 3.96 | 0 | Hydrophobic |
| C26 | CB | ALA- 31 | 3.78 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 64 | 4.08 | 0 | Hydrophobic |
| C24 | CB | PHE- 80 | 3.39 | 0 | Hydrophobic |
| C26 | CD2 | PHE- 80 | 3.21 | 0 | Hydrophobic |
| N04 | N | LEU- 83 | 3.38 | 160.13 | H-Bond (Protein Donor) |
| N10 | O | LEU- 83 | 2.82 | 136.62 | H-Bond (Ligand Donor) |
| C12 | CB | ASP- 86 | 4.45 | 0 | Hydrophobic |
| N15 | NZ | LYS- 89 | 2.63 | 159.08 | H-Bond (Protein Donor) |
| DuAr | NZ | LYS- 89 | 3.78 | 64.13 | Pi/Cation |
| C21 | CG | GLN- 131 | 3.52 | 0 | Hydrophobic |
| F27 | CB | ASN- 132 | 3.49 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 134 | 3.77 | 0 | Hydrophobic |
| F27 | CD2 | LEU- 134 | 4.12 | 0 | Hydrophobic |
| F27 | CB | ALA- 144 | 3.56 | 0 | Hydrophobic |
