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
2003-09-20
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 10.280 | 10.280 | 10.280 | 0.000 | 10.280 | 1 |
| Name: | Glycogen synthase kinase-3 beta |
|---|---|
| ID: | GSK3B_HUMAN |
| AC: | P49841 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.26 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 39.396 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.379 | 492.750 |
| % Hydrophobic | % Polar |
|---|---|
| 60.27 | 39.73 |
| According to VolSite | |
| HET Code: | DFN |
|---|---|
| Formula: | C22H20FN3O4 |
| Molecular weight: | 409.410 g/mol |
| DrugBank ID: | DB01772 |
| Buried Surface Area: | 69.72 % |
| Polar Surface area: | 103.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 64.2043 | 59.8477 | 10.219 |
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 |
| F39 | CG1 | ILE- 62 | 4.46 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 62 | 3.61 | 0 | Hydrophobic |
| F39 | CE1 | PHE- 67 | 3.34 | 0 | Hydrophobic |
| C26 | CE2 | PHE- 67 | 4.43 | 0 | Hydrophobic |
| C34 | CZ | PHE- 67 | 4.46 | 0 | Hydrophobic |
| C11 | CB | PHE- 67 | 3.95 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 70 | 3.69 | 0 | Hydrophobic |
| F39 | CB | VAL- 70 | 3.54 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 70 | 3.83 | 0 | Hydrophobic |
| C12 | CD | LYS- 85 | 3.98 | 0 | Hydrophobic |
| N04 | O | ASP- 133 | 2.75 | 149.47 | H-Bond (Ligand Donor) |
| O07 | N | VAL- 135 | 2.87 | 164.81 | H-Bond (Protein Donor) |
| C28 | CG2 | THR- 138 | 4.16 | 0 | Hydrophobic |
| C40 | CG2 | THR- 138 | 3.76 | 0 | Hydrophobic |
| O45 | O | GLN- 185 | 2.89 | 161.23 | H-Bond (Ligand Donor) |
| C40 | CD2 | LEU- 188 | 4.12 | 0 | Hydrophobic |
| C08 | CB | CYS- 199 | 4.32 | 0 | Hydrophobic |
| C26 | SG | CYS- 199 | 3.91 | 0 | Hydrophobic |
| C09 | SG | CYS- 199 | 3.62 | 0 | Hydrophobic |
| C11 | CB | ASP- 200 | 3.82 | 0 | Hydrophobic |
| N15 | O | HOH- 605 | 2.81 | 134.42 | H-Bond (Ligand Donor) |
