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
2008-06-04
| 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: | 22.012 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.771 | 840.375 |
| % Hydrophobic | % Polar |
|---|---|
| 45.38 | 54.62 |
| According to VolSite | |
| HET Code: | IM9 |
|---|---|
| Formula: | C23H30N7O2 |
| Molecular weight: | 436.530 g/mol |
| DrugBank ID: | DB07982 |
| Buried Surface Area: | 51.24 % |
| Polar Surface area: | 100.66 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 1.87256 | 26.5623 | 8.24903 |
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 |
| C27 | CB | ILE- 10 | 4.43 | 0 | Hydrophobic |
| C20 | CB | ILE- 10 | 4.12 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 10 | 3.63 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 18 | 4.01 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 18 | 3.6 | 0 | Hydrophobic |
| C11 | CB | ALA- 31 | 3.56 | 0 | Hydrophobic |
| N7 | NZ | LYS- 33 | 2.89 | 146.38 | H-Bond (Protein Donor) |
| DuAr | NZ | LYS- 33 | 3.98 | 101.8 | Pi/Cation |
| C11 | CG1 | VAL- 64 | 3.91 | 0 | Hydrophobic |
| C11 | CB | PHE- 80 | 4.07 | 0 | Hydrophobic |
| N13 | N | LEU- 83 | 3.08 | 175.74 | H-Bond (Protein Donor) |
| N15 | O | LEU- 83 | 2.72 | 148.19 | H-Bond (Ligand Donor) |
| C1 | CB | ASN- 132 | 4.24 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 134 | 3.55 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 134 | 3.65 | 0 | Hydrophobic |
| C6 | CB | ASP- 145 | 3.73 | 0 | Hydrophobic |
