sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2009-08-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.890 | 8.890 | 8.890 | 0.000 | 8.890 | 1 |
| Name: | Ribosomal protein S6 kinase beta-1 |
|---|---|
| ID: | KS6B1_HUMAN |
| AC: | P23443 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 54.377 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.465 | 688.500 |
| % Hydrophobic | % Polar |
|---|---|
| 57.35 | 42.65 |
| According to VolSite | |
| HET Code: | STU |
|---|---|
| Formula: | C28H27N4O3 |
| Molecular weight: | 467.539 g/mol |
| DrugBank ID: | DB02010 |
| Buried Surface Area: | 70.76 % |
| Polar Surface area: | 74.03 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 8 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -35.9558 | -28.6647 | 3.36509 |
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 |
| C25 | CB | LEU- 97 | 3.98 | 0 | Hydrophobic |
| C19 | CB | LEU- 97 | 4.4 | 0 | Hydrophobic |
| C20 | CB | LEU- 97 | 3.98 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 97 | 3.98 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 97 | 3.77 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 105 | 4.34 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 105 | 4.07 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 105 | 3.81 | 0 | Hydrophobic |
| C7 | CB | ALA- 121 | 4.15 | 0 | Hydrophobic |
| C14 | CD | LYS- 123 | 3.57 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 172 | 3.5 | 0 | Hydrophobic |
| N1 | O | GLU- 173 | 2.84 | 167.7 | H-Bond (Ligand Donor) |
| O5 | N | LEU- 175 | 2.65 | 154.38 | H-Bond (Protein Donor) |
| C24 | CG | GLU- 179 | 4.29 | 0 | Hydrophobic |
| C2 | CB | GLU- 179 | 3.92 | 0 | Hydrophobic |
| N4 | O | GLU- 222 | 2.85 | 155.47 | H-Bond (Ligand Donor) |
| C27 | CG | MET- 225 | 3.82 | 0 | Hydrophobic |
| C10 | SD | MET- 225 | 3.79 | 0 | Hydrophobic |
| C13 | CG2 | THR- 235 | 3.78 | 0 | Hydrophobic |
