sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2001-02-06
| 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: | 30.214 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.565 | 874.125 |
| % Hydrophobic | % Polar |
|---|---|
| 41.70 | 58.30 |
| According to VolSite | |
| HET Code: | 1PU |
|---|---|
| Formula: | C17H16N4O2 |
| Molecular weight: | 308.335 g/mol |
| DrugBank ID: | DB04186 |
| Buried Surface Area: | 61.45 % |
| Polar Surface area: | 74.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 6.09835 | 9.56939 | 26.2385 |
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 |
| C1 | CG2 | ILE- 10 | 4.3 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 10 | 4.38 | 0 | Hydrophobic |
| C23 | CG2 | ILE- 10 | 4.45 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 18 | 4.2 | 0 | Hydrophobic |
| C9 | CB | ALA- 31 | 3.43 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 64 | 3.66 | 0 | Hydrophobic |
| C14 | CB | PHE- 80 | 3.53 | 0 | Hydrophobic |
| N16 | O | VAL- 83 | 2.85 | 151.22 | H-Bond (Ligand Donor) |
| O17 | N | VAL- 83 | 2.83 | 157.3 | H-Bond (Protein Donor) |
| C23 | CB | ASP- 86 | 4 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 134 | 4.19 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 134 | 4.25 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 134 | 3.49 | 0 | Hydrophobic |
| C8 | CB | ALA- 144 | 4.2 | 0 | Hydrophobic |
