sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2000-10-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.750 | 5.750 | 5.750 | 0.000 | 5.750 | 1 |
| Name: | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform |
|---|---|
| ID: | PK3CG_HUMAN |
| AC: | P48736 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.1.153 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 47.400 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.330 | 634.500 |
| % Hydrophobic | % Polar |
|---|---|
| 45.21 | 54.79 |
| According to VolSite | |
| HET Code: | STU |
|---|---|
| Formula: | C28H27N4O3 |
| Molecular weight: | 467.539 g/mol |
| DrugBank ID: | DB02010 |
| Buried Surface Area: | 64.7 % |
| 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 |
|---|---|---|
| 44.1685 | 15.4877 | 31.5041 |
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 | SD | MET- 804 | 3.66 | 0 | Hydrophobic |
| C26 | SD | MET- 804 | 4.41 | 0 | Hydrophobic |
| C26 | CB | SER- 806 | 4.13 | 0 | Hydrophobic |
| C26 | CG | PRO- 810 | 3.71 | 0 | Hydrophobic |
| C2 | CZ3 | TRP- 812 | 3.5 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 831 | 4.47 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 831 | 3.71 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 879 | 3.83 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 879 | 3.68 | 0 | Hydrophobic |
| C4 | CG2 | ILE- 881 | 4.4 | 0 | Hydrophobic |
| O5 | N | VAL- 882 | 2.71 | 158.84 | H-Bond (Protein Donor) |
| C3 | CE | MET- 953 | 3.89 | 0 | Hydrophobic |
| C7 | SD | MET- 953 | 3.73 | 0 | Hydrophobic |
| C4 | CE | MET- 953 | 3.47 | 0 | Hydrophobic |
| C10 | CG2 | ILE- 963 | 4.28 | 0 | Hydrophobic |
| C13 | CB | ILE- 963 | 4.2 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 963 | 4.09 | 0 | Hydrophobic |
| C15 | CB | ASP- 964 | 4.29 | 0 | Hydrophobic |
