sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2013-09-08
| Name: | Na(+):neurotransmitter symporter (Snf family) |
|---|---|
| ID: | O67854_AQUAE |
| AC: | O67854 |
| Organism: | Aquifex aeolicus |
| Reign: | Bacteria |
| TaxID: | 224324 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 34.962 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | NA NA |
| Ligandability | Volume (Å3) |
|---|---|
| 1.121 | 735.750 |
| % Hydrophobic | % Polar |
|---|---|
| 59.63 | 40.37 |
| According to VolSite | |
| HET Code: | FVX |
|---|---|
| Formula: | C15H22F3N2O2 |
| Molecular weight: | 319.343 g/mol |
| DrugBank ID: | DB00176 |
| Buried Surface Area: | 73.5 % |
| Polar Surface area: | 58.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 187.934 | -16.3266 | 99.2647 |
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 |
| C7 | CE1 | TYR- 21 | 4.46 | 0 | Hydrophobic |
| C10 | CE1 | TYR- 21 | 4.07 | 0 | Hydrophobic |
| N12 | O | ALA- 22 | 3.21 | 133.29 | H-Bond (Ligand Donor) |
| N12 | OD1 | ASP- 24 | 2.97 | 124.02 | H-Bond (Ligand Donor) |
| N12 | OD1 | ASP- 24 | 2.97 | 0 | Ionic (Ligand Cationic) |
| F21 | CB | PRO- 101 | 4 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 104 | 4.04 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 104 | 4.18 | 0 | Hydrophobic |
| F21 | CB | VAL- 104 | 4.25 | 0 | Hydrophobic |
| F22 | CG1 | VAL- 104 | 3.8 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 104 | 3.58 | 0 | Hydrophobic |
| F22 | CB | ALA- 105 | 3.69 | 0 | Hydrophobic |
| C3 | CE1 | TYR- 107 | 4.32 | 0 | Hydrophobic |
| C3 | CD1 | TYR- 108 | 4.28 | 0 | Hydrophobic |
| C17 | CB | TYR- 108 | 4.4 | 0 | Hydrophobic |
| C19 | CD2 | TYR- 108 | 4.46 | 0 | Hydrophobic |
| F22 | CB | TYR- 108 | 3.33 | 0 | Hydrophobic |
| C1 | CE1 | PHE- 253 | 3.64 | 0 | Hydrophobic |
| C4 | CE1 | PHE- 253 | 4.04 | 0 | Hydrophobic |
| N12 | O | PHE- 253 | 2.85 | 149.13 | H-Bond (Ligand Donor) |
| C5 | CE1 | PHE- 259 | 3.29 | 0 | Hydrophobic |
| C6 | CZ | PHE- 259 | 3.24 | 0 | Hydrophobic |
| C14 | CB | PHE- 259 | 4.34 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 261 | 4.45 | 0 | Hydrophobic |
| C10 | CB | SER- 355 | 4.45 | 0 | Hydrophobic |
| C17 | CB | SER- 355 | 4.27 | 0 | Hydrophobic |
| F20 | CB | SER- 356 | 4.2 | 0 | Hydrophobic |
| C1 | CG2 | THR- 408 | 4.11 | 0 | Hydrophobic |
| C3 | CG2 | THR- 408 | 4.21 | 0 | Hydrophobic |
| C5 | CG2 | THR- 408 | 4.27 | 0 | Hydrophobic |
