sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2003-07-08
| 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: | 40.019 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.575 | 540.000 |
| % Hydrophobic | % Polar |
|---|---|
| 41.88 | 58.13 |
| According to VolSite | |
| HET Code: | PM1 |
|---|---|
| Formula: | C21H13F2N3O2 |
| Molecular weight: | 377.344 g/mol |
| DrugBank ID: | DB04006 |
| Buried Surface Area: | 68.06 % |
| Polar Surface area: | 77.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 13.0262 | -8.80104 | 24.9814 |
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 |
| C14 | CD1 | ILE- 10 | 4.41 | 0 | Hydrophobic |
| C15 | CG1 | ILE- 10 | 4 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 18 | 3.86 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 18 | 4.04 | 0 | Hydrophobic |
| F36 | CG2 | VAL- 18 | 3.35 | 0 | Hydrophobic |
| F36 | CG | LYS- 33 | 3.54 | 0 | Hydrophobic |
| C25 | CD | LYS- 33 | 4.03 | 0 | Hydrophobic |
| F36 | CE2 | PHE- 80 | 4.31 | 0 | Hydrophobic |
| N12 | N | LEU- 83 | 3.07 | 157.41 | H-Bond (Protein Donor) |
| C19 | CB | ASP- 86 | 4.26 | 0 | Hydrophobic |
| F39 | CB | ASN- 132 | 4.45 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 134 | 3.95 | 0 | Hydrophobic |
| F39 | CD2 | LEU- 134 | 4.07 | 0 | Hydrophobic |
| C29 | CB | ALA- 144 | 3.99 | 0 | Hydrophobic |
| C29 | CB | ASP- 145 | 3.52 | 0 | Hydrophobic |
| C28 | CB | ASP- 145 | 3.61 | 0 | Hydrophobic |
