sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2015-01-16
| Name: | Sodium-dependent dopamine transporter |
|---|---|
| ID: | DAT_DROME |
| AC: | Q7K4Y6 |
| Organism: | Drosophila melanogaster |
| Reign: | Eukaryota |
| TaxID: | 7227 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 65.273 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | NA NA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.997 | 1086.750 |
| % Hydrophobic | % Polar |
|---|---|
| 43.17 | 56.83 |
| According to VolSite | |
| HET Code: | COC |
|---|---|
| Formula: | C17H22NO4 |
| Molecular weight: | 304.361 g/mol |
| DrugBank ID: | DB00907 |
| Buried Surface Area: | 74.2 % |
| Polar Surface area: | 57.04 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 202.936 | 283.539 | 27.4669 |
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 |
| C21 | CE2 | PHE- 43 | 4.13 | 0 | Hydrophobic |
| C29 | CE1 | PHE- 43 | 3.82 | 0 | Hydrophobic |
| N12 | OD2 | ASP- 46 | 3.35 | 125.07 | H-Bond (Ligand Donor) |
| N12 | OD2 | ASP- 46 | 3.35 | 0 | Ionic (Ligand Cationic) |
| N12 | OD1 | ASP- 46 | 3.75 | 0 | Ionic (Ligand Cationic) |
| C5 | CB | ALA- 117 | 4.39 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 120 | 3.55 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 120 | 3.56 | 0 | Hydrophobic |
| C9 | CB | ASP- 121 | 3.21 | 0 | Hydrophobic |
| C1 | CZ | TYR- 123 | 4.26 | 0 | Hydrophobic |
| C1 | CD2 | TYR- 124 | 3.97 | 0 | Hydrophobic |
| C11 | CB | TYR- 124 | 3.97 | 0 | Hydrophobic |
| C18 | CE2 | PHE- 325 | 4.5 | 0 | Hydrophobic |
| C8 | CE2 | PHE- 325 | 3.72 | 0 | Hydrophobic |
| C26 | CB | SER- 421 | 3.84 | 0 | Hydrophobic |
| C11 | CB | SER- 422 | 4.42 | 0 | Hydrophobic |
