sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 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 |
|---|---|
| B | 100 % |
| B-Factor: | 37.280 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | NA NA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.970 | 1083.375 |
| % Hydrophobic | % Polar |
|---|---|
| 49.84 | 50.16 |
| According to VolSite | |
| HET Code: | 29Q |
|---|---|
| Formula: | C16H14ClN2O |
| Molecular weight: | 285.748 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.85 % |
| Polar Surface area: | 37.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -26.5843 | 16.2088 | 35.7067 |
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 |
| C3 | CE1 | TYR- 21 | 3.68 | 0 | Hydrophobic |
| C2 | CZ | TYR- 21 | 4.13 | 0 | Hydrophobic |
| O | OD2 | ASP- 24 | 2.68 | 168.43 | H-Bond (Ligand Donor) |
| C1 | OD2 | ASP- 24 | 3.24 | 0 | Ionic (Ligand Cationic) |
| C3 | CB | ASP- 24 | 4.27 | 0 | Hydrophobic |
| CL | CB | PRO- 101 | 4.42 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 104 | 4 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 104 | 3.52 | 0 | Hydrophobic |
| CL | CB | ALA- 105 | 3.8 | 0 | Hydrophobic |
| C | CE1 | TYR- 108 | 4.37 | 0 | Hydrophobic |
| C14 | CB | TYR- 108 | 3.98 | 0 | Hydrophobic |
| C9 | CB | PHE- 253 | 4.34 | 0 | Hydrophobic |
| N1 | O | PHE- 253 | 2.7 | 162.11 | H-Bond (Ligand Donor) |
| C9 | CZ | PHE- 259 | 3.44 | 0 | Hydrophobic |
| C15 | CB | SER- 355 | 4.3 | 0 | Hydrophobic |
| C | CB | SER- 355 | 4.46 | 0 | Hydrophobic |
| C3 | CB | SER- 355 | 3.99 | 0 | Hydrophobic |
