sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2008-10-23
| 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: | 48.553 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.540 | 560.250 |
| % Hydrophobic | % Polar |
|---|---|
| 46.99 | 53.01 |
| According to VolSite | |
| HET Code: | EZR |
|---|---|
| Formula: | C26H28N7O |
| Molecular weight: | 454.547 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.4 % |
| Polar Surface area: | 100.29 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 6 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 0.266206 | 29.6788 | 9.73132 |
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 |
| C22 | CG2 | ILE- 10 | 3.97 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 10 | 3.8 | 0 | Hydrophobic |
| C15 | CB | ALA- 31 | 3.59 | 0 | Hydrophobic |
| C26 | CD | LYS- 33 | 3.31 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 64 | 3.9 | 0 | Hydrophobic |
| C7 | CB | VAL- 64 | 4.4 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 64 | 3.57 | 0 | Hydrophobic |
| C26 | CE1 | PHE- 80 | 3.66 | 0 | Hydrophobic |
| C4 | CB | PHE- 80 | 4.4 | 0 | Hydrophobic |
| C8 | CB | PHE- 80 | 3.47 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 80 | 3.35 | 0 | Aromatic Face/Face |
| N30 | O | GLU- 81 | 2.62 | 169.43 | H-Bond (Ligand Donor) |
| N28 | N | LEU- 83 | 3.27 | 167.61 | H-Bond (Protein Donor) |
| N29 | O | LEU- 83 | 2.65 | 122.11 | H-Bond (Ligand Donor) |
| C21 | CB | ASP- 86 | 3.89 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 134 | 4.12 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 134 | 3.28 | 0 | Hydrophobic |
| C11 | CB | ALA- 144 | 3.83 | 0 | Hydrophobic |
| C4 | CB | ALA- 144 | 3.59 | 0 | Hydrophobic |
| C9 | CB | ASP- 145 | 4.23 | 0 | Hydrophobic |
