sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2011-04-17
| 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: | 25.635 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.706 | 668.250 |
| % Hydrophobic | % Polar |
|---|---|
| 44.44 | 55.56 |
| According to VolSite | |
| HET Code: | 09Z |
|---|---|
| Formula: | C12H14N4OS |
| Molecular weight: | 262.331 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.01 % |
| Polar Surface area: | 109.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -39.8652 | -80.3359 | -85.0729 |
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 |
| S9 | CG2 | ILE- 10 | 3.64 | 0 | Hydrophobic |
| C2 | CG2 | ILE- 10 | 3.41 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 18 | 4.47 | 0 | Hydrophobic |
| N16 | NZ | LYS- 33 | 3.11 | 173.37 | H-Bond (Protein Donor) |
| N10 | O | GLU- 81 | 2.86 | 149.74 | H-Bond (Ligand Donor) |
| C1 | CZ | PHE- 82 | 3.96 | 0 | Hydrophobic |
| C2 | CE2 | PHE- 82 | 4.4 | 0 | Hydrophobic |
| N4 | O | LEU- 83 | 2.85 | 125.92 | H-Bond (Ligand Donor) |
| N6 | N | LEU- 83 | 3.43 | 170.93 | H-Bond (Protein Donor) |
| C3 | CB | ASP- 86 | 4.07 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 134 | 3.99 | 0 | Hydrophobic |
| S9 | CD1 | LEU- 134 | 4.09 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 134 | 4.47 | 0 | Hydrophobic |
| C13 | CB | ALA- 144 | 4.21 | 0 | Hydrophobic |
| C14 | CB | ASP- 145 | 3.91 | 0 | Hydrophobic |
