sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2012-11-05
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.960 | 9.960 | 9.960 | 0.000 | 9.960 | 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: | 48.982 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.850 | 702.000 |
| % Hydrophobic | % Polar |
|---|---|
| 49.04 | 50.96 |
| According to VolSite | |
| HET Code: | 19P |
|---|---|
| Formula: | C24H26N6O3 |
| Molecular weight: | 446.502 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 55.52 % |
| Polar Surface area: | 102.76 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 44.1204 | 15.3209 | 31.7049 |
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 |
| C26 | SD | MET- 804 | 4.46 | 0 | Hydrophobic |
| C28 | CZ3 | TRP- 812 | 3.24 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 831 | 4.5 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 831 | 4.44 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 831 | 3.75 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 831 | 3.54 | 0 | Hydrophobic |
| C17 | CB | ASP- 836 | 4.33 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 838 | 4.31 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 879 | 3.98 | 0 | Hydrophobic |
| C2 | CG2 | ILE- 879 | 3.45 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 879 | 3.68 | 0 | Hydrophobic |
| N7 | N | VAL- 882 | 3.46 | 169.01 | H-Bond (Protein Donor) |
| C9 | CE | MET- 953 | 3.68 | 0 | Hydrophobic |
| C10 | SD | MET- 953 | 3.91 | 0 | Hydrophobic |
| C28 | CE | MET- 953 | 3.97 | 0 | Hydrophobic |
| C11 | CB | ILE- 963 | 4.17 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 963 | 3.64 | 0 | Hydrophobic |
| C2 | CG2 | ILE- 963 | 3.9 | 0 | Hydrophobic |
| N13 | N | ASP- 964 | 3.04 | 134.67 | H-Bond (Protein Donor) |
| C17 | CB | ASP- 964 | 3.87 | 0 | Hydrophobic |
| O32 | OD1 | ASP- 964 | 3.34 | 134.58 | H-Bond (Ligand Donor) |
