sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2009-04-05
| Name: | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily |
|---|---|
| ID: | Q9XZJ5_STRER |
| AC: | Q9XZJ5 |
| Organism: | Strongyloides stercoralis |
| Reign: | Eukaryota |
| TaxID: | 6248 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 20.891 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.880 | 540.000 |
| % Hydrophobic | % Polar |
|---|---|
| 74.38 | 25.63 |
| According to VolSite | |
| HET Code: | DL4 |
|---|---|
| Formula: | C27H41O3 |
| Molecular weight: | 413.613 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.75 % |
| Polar Surface area: | 57.2 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -4.574 | -35.8926 | -0.46 |
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 |
| C26 | CD1 | LEU- 545 | 3.96 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 545 | 4.15 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 555 | 3.87 | 0 | Hydrophobic |
| C7 | CG2 | ILE- 555 | 4.43 | 0 | Hydrophobic |
| C22 | CG1 | VAL- 558 | 4.39 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 558 | 4.09 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 558 | 3.79 | 0 | Hydrophobic |
| C15 | CG | MET- 559 | 4.24 | 0 | Hydrophobic |
| C18 | CE | MET- 559 | 3.99 | 0 | Hydrophobic |
| C19 | CE | MET- 559 | 3.69 | 0 | Hydrophobic |
| C6 | CE | MET- 559 | 3.88 | 0 | Hydrophobic |
| C26 | CB | ILE- 561 | 3.76 | 0 | Hydrophobic |
| O2 | OG1 | THR- 562 | 3.18 | 155.56 | H-Bond (Protein Donor) |
| C19 | CG2 | ILE- 593 | 4.34 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 596 | 4.3 | 0 | Hydrophobic |
| C19 | CB | LEU- 596 | 4.4 | 0 | Hydrophobic |
| C1 | CG2 | THR- 597 | 4.1 | 0 | Hydrophobic |
| O2 | CZ | ARG- 599 | 3.67 | 0 | Ionic (Protein Cationic) |
| O2 | NH1 | ARG- 599 | 2.9 | 153.29 | H-Bond (Protein Donor) |
| C21 | CG | ARG- 599 | 3.67 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 603 | 4.28 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 603 | 3.91 | 0 | Hydrophobic |
| C22 | CB | TRP- 611 | 4.21 | 0 | Hydrophobic |
| C17 | CD2 | TRP- 611 | 4.25 | 0 | Hydrophobic |
| C14 | CH2 | TRP- 611 | 4.3 | 0 | Hydrophobic |
| C12 | CE2 | TRP- 611 | 4.11 | 0 | Hydrophobic |
| C25 | CB | THR- 613 | 4.46 | 0 | Hydrophobic |
| C24 | CG2 | THR- 613 | 3.75 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 621 | 3.92 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 621 | 4.04 | 0 | Hydrophobic |
| C7 | CE | MET- 625 | 3.6 | 0 | Hydrophobic |
| O1 | NE2 | GLN- 637 | 2.6 | 144.77 | H-Bond (Protein Donor) |
| C1 | CD1 | PHE- 641 | 4.1 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 724 | 4.21 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 731 | 4.41 | 0 | Hydrophobic |
| C19 | CZ | PHE- 749 | 4.48 | 0 | Hydrophobic |
