sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.140 Å
X-ray
2009-04-01
| 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: | 26.012 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 19 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.644 | 354.375 |
| % Hydrophobic | % Polar |
|---|---|
| 55.24 | 44.76 |
| According to VolSite | |
| HET Code: | SRE |
|---|---|
| Formula: | C17H18Cl2N |
| Molecular weight: | 307.238 g/mol |
| DrugBank ID: | DB01104 |
| Buried Surface Area: | 58.37 % |
| Polar Surface area: | 16.61 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 0 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 26.9613 | 21.5395 | 24.0018 |
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 |
| CL19 | CB | LEU- 25 | 3.98 | 0 | Hydrophobic |
| CL20 | CB | LEU- 25 | 4.21 | 0 | Hydrophobic |
| CL20 | CB | LEU- 29 | 3.44 | 0 | Hydrophobic |
| CL20 | CB | ARG- 30 | 4.12 | 0 | Hydrophobic |
| C3 | CG | ARG- 30 | 4.29 | 0 | Hydrophobic |
| C14 | CG | ARG- 30 | 3.9 | 0 | Hydrophobic |
| CL19 | CE1 | TYR- 108 | 3.67 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 111 | 4.48 | 0 | Hydrophobic |
| CL19 | CD1 | ILE- 111 | 4.06 | 0 | Hydrophobic |
| CL19 | CZ | PHE- 253 | 3.64 | 0 | Hydrophobic |
| C14 | CB | ALA- 319 | 4.28 | 0 | Hydrophobic |
| C6 | CB | ALA- 319 | 3.27 | 0 | Hydrophobic |
| CL20 | CE1 | PHE- 320 | 4.28 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 400 | 3.67 | 0 | Hydrophobic |
| C8 | CB | ASP- 401 | 4.03 | 0 | Hydrophobic |
| C18 | CB | ASP- 404 | 4.45 | 0 | Hydrophobic |
| N11 | OD2 | ASP- 404 | 2.71 | 155.78 | H-Bond (Ligand Donor) |
| N11 | OD2 | ASP- 404 | 2.71 | 0 | Ionic (Ligand Cationic) |
