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
2011-02-23
| 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: | 26.779 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.676 | 621.000 |
| % Hydrophobic | % Polar |
|---|---|
| 45.65 | 54.35 |
| According to VolSite | |
| HET Code: | X36 |
|---|---|
| Formula: | C16H13N3OS |
| Molecular weight: | 295.359 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.47 % |
| Polar Surface area: | 96.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 92.3877 | 80.468 | -48.6905 |
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 |
| S13 | CD1 | ILE- 10 | 3.89 | 0 | Hydrophobic |
| C20 | CB | ILE- 10 | 4.05 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 10 | 3.96 | 0 | Hydrophobic |
| C10 | CB | VAL- 18 | 4.08 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 18 | 3.76 | 0 | Hydrophobic |
| C10 | CD | LYS- 33 | 4.37 | 0 | Hydrophobic |
| N3 | O | GLU- 81 | 2.63 | 141.16 | H-Bond (Ligand Donor) |
| N1 | N | LEU- 83 | 3.17 | 171.33 | H-Bond (Protein Donor) |
| N15 | O | LEU- 83 | 2.92 | 152.71 | H-Bond (Ligand Donor) |
| C19 | CD | LYS- 89 | 3.91 | 0 | Hydrophobic |
| C8 | CB | ASN- 132 | 4.29 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 134 | 4.42 | 0 | Hydrophobic |
| S13 | CD2 | LEU- 134 | 3.95 | 0 | Hydrophobic |
| C7 | CB | ALA- 144 | 4.42 | 0 | Hydrophobic |
| C9 | CB | ASP- 145 | 3.62 | 0 | Hydrophobic |
