sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2012-06-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.000 | 9.000 | 9.000 | 0.000 | 9.000 | 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: | 57.618 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.909 | 820.125 |
| % Hydrophobic | % Polar |
|---|---|
| 48.97 | 51.03 |
| According to VolSite | |
| HET Code: | 14K |
|---|---|
| Formula: | C22H29FN9O3S |
| Molecular weight: | 518.588 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.48 % |
| Polar Surface area: | 161.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 22.3307 | 15.7293 | 21.2552 |
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 |
| O35 | NZ | LYS- 802 | 3.03 | 136.94 | H-Bond (Protein Donor) |
| C5 | CE | MET- 804 | 4.3 | 0 | Hydrophobic |
| C30 | CE | MET- 804 | 4.15 | 0 | Hydrophobic |
| C28 | CE | MET- 804 | 4.22 | 0 | Hydrophobic |
| O34 | N | ALA- 805 | 2.76 | 158 | H-Bond (Protein Donor) |
| F16 | CG | PRO- 810 | 4.4 | 0 | Hydrophobic |
| C28 | CZ3 | TRP- 812 | 4.29 | 0 | Hydrophobic |
| F16 | CG2 | ILE- 831 | 4.43 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 831 | 4.19 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 831 | 3.85 | 0 | Hydrophobic |
| O14 | NZ | LYS- 833 | 3.29 | 172.87 | H-Bond (Protein Donor) |
| F16 | CD | LYS- 833 | 3.32 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 838 | 3.79 | 0 | Hydrophobic |
| C23 | CG | TYR- 867 | 3.43 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 879 | 4.42 | 0 | Hydrophobic |
| C23 | CG2 | ILE- 879 | 3.9 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 882 | 4.09 | 0 | Hydrophobic |
| N20 | N | VAL- 882 | 3.03 | 159.06 | H-Bond (Protein Donor) |
| N24 | O | VAL- 882 | 2.79 | 155.34 | H-Bond (Ligand Donor) |
| C36 | CG2 | THR- 887 | 3.69 | 0 | Hydrophobic |
| C4 | SD | MET- 953 | 3.68 | 0 | Hydrophobic |
| C23 | CG2 | ILE- 963 | 4.34 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 963 | 3.64 | 0 | Hydrophobic |
| N24 | O | HOH- 1329 | 3.35 | 121.98 | H-Bond (Ligand Donor) |
