sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2011-04-22
| 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: | 32.239 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.844 | 627.750 |
| % Hydrophobic | % Polar |
|---|---|
| 44.62 | 55.38 |
| According to VolSite | |
| HET Code: | 21Z |
|---|---|
| Formula: | C16H14N4O3S2 |
| Molecular weight: | 374.437 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 54.55 % |
| Polar Surface area: | 164.79 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -38.4576 | 117.553 | 83.2341 |
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 |
| C12 | CB | ILE- 10 | 4.26 | 0 | Hydrophobic |
| S24 | CD1 | ILE- 10 | 4.18 | 0 | Hydrophobic |
| C09 | CD1 | ILE- 10 | 4.05 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 18 | 3.46 | 0 | Hydrophobic |
| N03 | O | GLU- 81 | 2.83 | 142.55 | H-Bond (Ligand Donor) |
| N01 | N | LEU- 83 | 3.3 | 170.24 | H-Bond (Protein Donor) |
| N02 | O | LEU- 83 | 2.69 | 145.36 | H-Bond (Ligand Donor) |
| C14 | CB | ASP- 86 | 4.27 | 0 | Hydrophobic |
| C17 | CB | ASN- 132 | 4.12 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 134 | 4.13 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 134 | 4.33 | 0 | Hydrophobic |
| S24 | CD1 | LEU- 134 | 4.03 | 0 | Hydrophobic |
| C16 | CB | ALA- 144 | 3.99 | 0 | Hydrophobic |
| C18 | CB | ASP- 145 | 3.37 | 0 | Hydrophobic |
