sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.860 Å
X-ray
2011-02-15
| 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: | 25.745 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.037 | 624.375 |
| % Hydrophobic | % Polar |
|---|---|
| 51.35 | 48.65 |
| According to VolSite | |
| HET Code: | X02 |
|---|---|
| Formula: | C13H13N3OS |
| Molecular weight: | 259.327 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.7 % |
| Polar Surface area: | 96.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 66.9021 | 152.62 | -48.6826 |
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 | CG2 | ILE- 10 | 3.5 | 0 | Hydrophobic |
| S9 | CG2 | ILE- 10 | 4.05 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 18 | 4.01 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 18 | 3.51 | 0 | Hydrophobic |
| S9 | CB | ALA- 31 | 4.34 | 0 | Hydrophobic |
| C16 | CD | LYS- 33 | 4.46 | 0 | Hydrophobic |
| N10 | O | GLU- 81 | 2.67 | 146.06 | H-Bond (Ligand Donor) |
| C3 | CE2 | PHE- 82 | 3.85 | 0 | Hydrophobic |
| N4 | O | LEU- 83 | 2.71 | 146.58 | H-Bond (Ligand Donor) |
| N6 | N | LEU- 83 | 3.27 | 176.13 | H-Bond (Protein Donor) |
| S9 | CD1 | LEU- 134 | 3.94 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 134 | 4.47 | 0 | Hydrophobic |
| C13 | CB | ALA- 144 | 4.39 | 0 | Hydrophobic |
| C15 | CB | ASP- 145 | 3.6 | 0 | Hydrophobic |
