sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2012-04-14
| 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 |
|---|---|
| C | 100 % |
| B-Factor: | 48.371 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.623 | 482.625 |
| % Hydrophobic | % Polar |
|---|---|
| 53.15 | 46.85 |
| According to VolSite | |
| HET Code: | 1RO |
|---|---|
| Formula: | C18H14N3OS2 |
| Molecular weight: | 352.453 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 72.85 % |
| Polar Surface area: | 109.5 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -36.3303 | 12.8575 | 38.8548 |
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 |
| C7 | CD1 | ILE- 10 | 3.85 | 0 | Hydrophobic |
| S2 | CG2 | VAL- 18 | 3.69 | 0 | Hydrophobic |
| S1 | CG2 | VAL- 18 | 3.92 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 18 | 4.46 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 18 | 4.08 | 0 | Hydrophobic |
| C2 | CB | ALA- 31 | 3.91 | 0 | Hydrophobic |
| C6 | CB | ALA- 31 | 3.49 | 0 | Hydrophobic |
| S1 | CD | LYS- 33 | 4.45 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 64 | 3.97 | 0 | Hydrophobic |
| C11 | CD1 | PHE- 80 | 3.93 | 0 | Hydrophobic |
| C6 | CB | PHE- 80 | 3.82 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 83 | 3.89 | 0 | Hydrophobic |
| N1 | N | LEU- 83 | 2.8 | 151.67 | H-Bond (Protein Donor) |
| C3 | CD2 | LEU- 134 | 3.87 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 134 | 3.47 | 0 | Hydrophobic |
| N3 | OD1 | ASP- 145 | 2.58 | 131.53 | H-Bond (Ligand Donor) |
| C18 | CB | ASP- 145 | 3.98 | 0 | Hydrophobic |
| S1 | CB | ASP- 145 | 4.31 | 0 | Hydrophobic |
