sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2005-11-03
| 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: | 46.859 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.454 | 492.750 |
| % Hydrophobic | % Polar |
|---|---|
| 47.95 | 52.05 |
| According to VolSite | |
| HET Code: | MTW |
|---|---|
| Formula: | C19H16N7O2 |
| Molecular weight: | 374.376 g/mol |
| DrugBank ID: | DB08218 |
| Buried Surface Area: | 77.28 % |
| Polar Surface area: | 115.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 26.1331 | 27.7289 | 27.1526 |
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 |
| C16 | CB | ILE- 10 | 4.46 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 10 | 3.66 | 0 | Hydrophobic |
| C8 | CB | ALA- 31 | 3.69 | 0 | Hydrophobic |
| N2 | NZ | LYS- 33 | 3.1 | 130.05 | H-Bond (Protein Donor) |
| C18 | CD | LYS- 33 | 4.38 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 64 | 3.75 | 0 | Hydrophobic |
| C8 | CB | PHE- 80 | 4.02 | 0 | Hydrophobic |
| N4 | N | LEU- 83 | 2.87 | 169.29 | H-Bond (Protein Donor) |
| N5 | O | LEU- 83 | 2.59 | 140.2 | H-Bond (Ligand Donor) |
| C13 | CG | GLN- 85 | 4.18 | 0 | Hydrophobic |
| C2 | CB | ASN- 132 | 3.95 | 0 | Hydrophobic |
| C8 | CG | LEU- 134 | 4.32 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 134 | 4.11 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 134 | 3.7 | 0 | Hydrophobic |
| C17 | CB | ALA- 144 | 4.13 | 0 | Hydrophobic |
