sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2005-01-10
| 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: | 35.132 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.512 | 864.000 |
| % Hydrophobic | % Polar |
|---|---|
| 59.38 | 40.63 |
| According to VolSite | |
| HET Code: | BRY |
|---|---|
| Formula: | C16H9BrN2O2 |
| Molecular weight: | 341.159 g/mol |
| DrugBank ID: | DB07493 |
| Buried Surface Area: | 62.52 % |
| Polar Surface area: | 58.2 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 25.6524 | 6.37086 | 8.43252 |
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 |
| C3 | CD1 | ILE- 10 | 4.18 | 0 | Hydrophobic |
| C11 | CB | ILE- 10 | 3.96 | 0 | Hydrophobic |
| BR1 | CG2 | VAL- 18 | 3.59 | 0 | Hydrophobic |
| C22 | CG1 | VAL- 18 | 3.75 | 0 | Hydrophobic |
| C18 | CB | ALA- 31 | 3.93 | 0 | Hydrophobic |
| C19 | CB | ALA- 31 | 3.89 | 0 | Hydrophobic |
| BR1 | CD | LYS- 33 | 3.73 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 64 | 3.91 | 0 | Hydrophobic |
| C19 | CB | PHE- 80 | 3.29 | 0 | Hydrophobic |
| N16 | O | GLU- 81 | 2.98 | 160.75 | H-Bond (Ligand Donor) |
| N4 | O | LEU- 83 | 3.06 | 148.97 | H-Bond (Ligand Donor) |
| C18 | CD1 | LEU- 134 | 3.8 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 134 | 4.11 | 0 | Hydrophobic |
| BR1 | CB | ASP- 145 | 3.55 | 0 | Hydrophobic |
