sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.260 Å
X-ray
2012-10-02
| 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: | 42.389 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.731 | 540.000 |
| % Hydrophobic | % Polar |
|---|---|
| 48.75 | 51.25 |
| According to VolSite | |
| HET Code: | T3C |
|---|---|
| Formula: | C21H25N8S |
| Molecular weight: | 421.542 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.67 % |
| Polar Surface area: | 134.6 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 5.7105 | 22.6061 | 22.6088 |
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 |
| C24 | CD1 | ILE- 10 | 4.33 | 0 | Hydrophobic |
| C18 | CG2 | ILE- 10 | 3.4 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 10 | 3.32 | 0 | Hydrophobic |
| C06 | CG1 | VAL- 18 | 3.81 | 0 | Hydrophobic |
| C06 | CB | ALA- 31 | 4.47 | 0 | Hydrophobic |
| C27 | CB | ALA- 31 | 3.93 | 0 | Hydrophobic |
| C06 | CD2 | PHE- 80 | 3.69 | 0 | Hydrophobic |
| N25 | N | LEU- 83 | 3.14 | 172.69 | H-Bond (Protein Donor) |
| N21 | OD2 | ASP- 86 | 3.81 | 0 | Ionic (Ligand Cationic) |
| C23 | CB | ASP- 86 | 3.74 | 0 | Hydrophobic |
| C15 | CE | LYS- 89 | 3.99 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 134 | 4.07 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 134 | 4.42 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 134 | 3.25 | 0 | Hydrophobic |
| S30 | CD1 | LEU- 134 | 4.22 | 0 | Hydrophobic |
| C01 | CB | ASP- 145 | 4.25 | 0 | Hydrophobic |
| N02 | OD2 | ASP- 145 | 2.78 | 121.04 | H-Bond (Ligand Donor) |
