sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2005-10-30
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.600 | 6.630 | 6.630 | 0.030 | 6.660 | 2 |
| 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 |
|---|---|
| C | 100 % |
| B-Factor: | 34.984 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.064 | 509.625 |
| % Hydrophobic | % Polar |
|---|---|
| 51.66 | 48.34 |
| According to VolSite | |
| HET Code: | CK8 |
|---|---|
| Formula: | C17H19N5S |
| Molecular weight: | 325.431 g/mol |
| DrugBank ID: | DB07562 |
| Buried Surface Area: | 56.61 % |
| Polar Surface area: | 82.18 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 46.272 | 47.1047 | 24.1057 |
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 |
| C6A | CG1 | ILE- 10 | 4.46 | 0 | Hydrophobic |
| C1B | CD1 | ILE- 10 | 4.08 | 0 | Hydrophobic |
| C6B | CG1 | ILE- 10 | 4.03 | 0 | Hydrophobic |
| C5B | CB | ILE- 10 | 3.94 | 0 | Hydrophobic |
| C6A | CG1 | VAL- 18 | 4.36 | 0 | Hydrophobic |
| C7A | CG2 | VAL- 18 | 4.38 | 0 | Hydrophobic |
| C5 | CB | ALA- 31 | 3.51 | 0 | Hydrophobic |
| C7A | CD | LYS- 33 | 3.76 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 64 | 4.42 | 0 | Hydrophobic |
| C5 | CB | PHE- 80 | 4.29 | 0 | Hydrophobic |
| N1 | N | LEU- 83 | 3.04 | 169.99 | H-Bond (Protein Donor) |
| N7 | O | LEU- 83 | 2.8 | 158.35 | H-Bond (Ligand Donor) |
| C9B | CB | GLN- 85 | 4.28 | 0 | Hydrophobic |
| C3B | CB | GLN- 85 | 3.84 | 0 | Hydrophobic |
| C8B | CD | LYS- 89 | 3.88 | 0 | Hydrophobic |
| C9B | CD | LYS- 89 | 4.15 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 134 | 3.33 | 0 | Hydrophobic |
| C7A | CB | ASP- 145 | 4.41 | 0 | Hydrophobic |
