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
2005-01-18
| 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: | 34.034 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.693 | 779.625 |
| % Hydrophobic | % Polar |
|---|---|
| 35.06 | 64.94 |
| According to VolSite | |
| HET Code: | 628 |
|---|---|
| Formula: | C20H15Cl2N4O3S |
| Molecular weight: | 462.329 g/mol |
| DrugBank ID: | DB04607 |
| Buried Surface Area: | 65.7 % |
| Polar Surface area: | 116.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 1.25607 | 29.0089 | 8.86657 |
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 |
| C17 | CD1 | ILE- 10 | 4.34 | 0 | Hydrophobic |
| C28 | CG2 | VAL- 18 | 3.53 | 0 | Hydrophobic |
| CL1 | CB | LYS- 33 | 3.55 | 0 | Hydrophobic |
| C28 | CD | LYS- 33 | 4.2 | 0 | Hydrophobic |
| CL1 | CE2 | PHE- 80 | 4.22 | 0 | Hydrophobic |
| N12 | N | LEU- 83 | 2.82 | 145.62 | H-Bond (Protein Donor) |
| C19 | CB | ASP- 86 | 3.98 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 86 | 3.47 | 152.63 | H-Bond (Ligand Donor) |
| O1 | N | ASP- 86 | 3.02 | 157.63 | H-Bond (Protein Donor) |
| C18 | CD2 | LEU- 134 | 4.2 | 0 | Hydrophobic |
| CL2 | CD2 | LEU- 134 | 4.36 | 0 | Hydrophobic |
| CL2 | CB | ALA- 144 | 3.22 | 0 | Hydrophobic |
| C25 | CB | ASP- 145 | 4.44 | 0 | Hydrophobic |
| O34 | O | HOH- 337 | 3.39 | 159.73 | H-Bond (Protein Donor) |
