sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2010-12-10
| 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: | 23.341 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.226 | 526.500 |
| % Hydrophobic | % Polar |
|---|---|
| 58.97 | 41.03 |
| According to VolSite | |
| HET Code: | JWS |
|---|---|
| Formula: | C10H11N5O2 |
| Molecular weight: | 233.227 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.05 % |
| Polar Surface area: | 120.17 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 64.7605 | 80.5418 | -84.826 |
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 |
| C6 | CD1 | ILE- 10 | 4.29 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 18 | 3.84 | 0 | Hydrophobic |
| C9 | CB | ALA- 31 | 3.41 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 64 | 3.95 | 0 | Hydrophobic |
| C17 | CE2 | PHE- 80 | 3.24 | 0 | Hydrophobic |
| C10 | CB | PHE- 80 | 3.72 | 0 | Hydrophobic |
| O8 | N | LEU- 83 | 2.76 | 168.48 | H-Bond (Protein Donor) |
| O8 | O | LEU- 83 | 3.09 | 124.91 | H-Bond (Ligand Donor) |
| N16 | O | LEU- 83 | 2.97 | 152.87 | H-Bond (Ligand Donor) |
| C11 | CD2 | LEU- 134 | 4.43 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 134 | 3.71 | 0 | Hydrophobic |
| C7 | CG | LEU- 134 | 3.84 | 0 | Hydrophobic |
| C17 | CB | ALA- 144 | 3.57 | 0 | Hydrophobic |
| C10 | CB | ALA- 144 | 4.06 | 0 | Hydrophobic |
| N1 | O | HOH- 387 | 2.75 | 179.97 | H-Bond (Protein Donor) |
