sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2013-06-04
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.470 | 8.720 | 8.820 | 0.160 | 8.890 | 12 |
| Name: | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform |
|---|---|
| ID: | PK3CA_HUMAN |
| AC: | P42336 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 37.708 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.221 | 469.125 |
| % Hydrophobic | % Polar |
|---|---|
| 60.43 | 39.57 |
| According to VolSite | |
| HET Code: | X6K |
|---|---|
| Formula: | C19H16N4O3 |
| Molecular weight: | 348.355 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.97 % |
| Polar Surface area: | 84.51 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 31.812 | 45.7778 | 42.1677 |
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 |
| C05 | CE | MET- 772 | 3.67 | 0 | Hydrophobic |
| C17 | CH2 | TRP- 780 | 4.4 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 800 | 4.27 | 0 | Hydrophobic |
| C22 | CD | LYS- 802 | 4.37 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 807 | 3.9 | 0 | Hydrophobic |
| C13 | CE2 | TYR- 836 | 4.25 | 0 | Hydrophobic |
| C14 | CG | TYR- 836 | 4.05 | 0 | Hydrophobic |
| O25 | OH | TYR- 836 | 2.97 | 171.38 | H-Bond (Protein Donor) |
| C13 | CG2 | ILE- 848 | 3.84 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 848 | 3.53 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 850 | 4.25 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 851 | 3.6 | 0 | Hydrophobic |
| C16 | CB | VAL- 851 | 3.97 | 0 | Hydrophobic |
| O15 | N | VAL- 851 | 2.51 | 164.86 | H-Bond (Protein Donor) |
| C16 | SD | MET- 922 | 4.07 | 0 | Hydrophobic |
| C14 | CE2 | PHE- 930 | 4.25 | 0 | Hydrophobic |
| C05 | CD1 | ILE- 932 | 4.02 | 0 | Hydrophobic |
| C26 | CB | ILE- 932 | 4.14 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 932 | 4.14 | 0 | Hydrophobic |
| C21 | CB | ASP- 933 | 4.07 | 0 | Hydrophobic |
