sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 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: | 41.988 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | NA NA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.774 | 823.500 |
| % Hydrophobic | % Polar |
|---|---|
| 55.33 | 44.67 |
| According to VolSite | |
| HET Code: | 29E |
|---|---|
| Formula: | C18H20NOS |
| Molecular weight: | 298.422 g/mol |
| DrugBank ID: | DB00476 |
| Buried Surface Area: | 74.33 % |
| Polar Surface area: | 54.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 99.2972 | 14.7943 | 34.5034 |
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 |
| N | O | TYR- 21 | 2.92 | 149.85 | H-Bond (Ligand Donor) |
| C3 | CE1 | TYR- 21 | 4.43 | 0 | Hydrophobic |
| N | OD1 | ASP- 24 | 2.62 | 169.9 | H-Bond (Ligand Donor) |
| N | OD1 | ASP- 24 | 2.62 | 0 | Ionic (Ligand Cationic) |
| C2 | CB | ASP- 24 | 4.43 | 0 | Hydrophobic |
| C7 | CB | PRO- 101 | 3.5 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 104 | 3.46 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 104 | 3.47 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 104 | 3.47 | 0 | Hydrophobic |
| C10 | CB | ALA- 105 | 3.54 | 0 | Hydrophobic |
| C11 | CD2 | TYR- 108 | 3.36 | 0 | Hydrophobic |
| C11 | CB | TYR- 108 | 3.85 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 109 | 4.46 | 0 | Hydrophobic |
| S | CZ | PHE- 259 | 3.45 | 0 | Hydrophobic |
| C6 | CB | PHE- 259 | 3.66 | 0 | Hydrophobic |
| C6 | CD1 | PHE- 259 | 3.41 | 0 | Hydrophobic |
| C11 | CB | SER- 356 | 3.6 | 0 | Hydrophobic |
| C10 | CG | MET- 360 | 4.4 | 0 | Hydrophobic |
