sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.350 Å
X-ray
2007-08-29
| 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: | 20.929 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.778 | 695.250 |
| % Hydrophobic | % Polar |
|---|---|
| 45.63 | 54.37 |
| According to VolSite | |
| HET Code: | 5SC |
|---|---|
| Formula: | C19H16BrN5O |
| Molecular weight: | 410.267 g/mol |
| DrugBank ID: | DB07179 |
| Buried Surface Area: | 69.29 % |
| Polar Surface area: | 67.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 1.665 | 27.4136 | 7.70731 |
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 |
| C13 | CD1 | ILE- 10 | 4.29 | 0 | Hydrophobic |
| C17 | CB | ILE- 10 | 3.86 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 18 | 3.82 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 18 | 3.86 | 0 | Hydrophobic |
| BR24 | CB | ALA- 31 | 4.27 | 0 | Hydrophobic |
| N06 | NZ | LYS- 33 | 3.1 | 145.43 | H-Bond (Protein Donor) |
| BR24 | CG1 | VAL- 64 | 3.87 | 0 | Hydrophobic |
| BR24 | CG | PHE- 80 | 3.52 | 0 | Hydrophobic |
| N04 | N | LEU- 83 | 3.28 | 165.33 | H-Bond (Protein Donor) |
| N10 | O | LEU- 83 | 2.79 | 139.17 | H-Bond (Ligand Donor) |
| C20 | CG | GLN- 131 | 3.41 | 0 | Hydrophobic |
| C25 | CB | ASN- 132 | 3.81 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 134 | 4.21 | 0 | Hydrophobic |
| BR24 | CD1 | LEU- 134 | 4.47 | 0 | Hydrophobic |
| BR24 | CB | ALA- 144 | 4.07 | 0 | Hydrophobic |
| C25 | CB | ALA- 144 | 4.07 | 0 | Hydrophobic |
