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: | 51.579 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.670 | 648.000 |
| % Hydrophobic | % Polar |
|---|---|
| 68.23 | 31.77 |
| According to VolSite | |
| HET Code: | DL7 |
|---|---|
| Formula: | C27H41O3 |
| Molecular weight: | 413.613 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.33 % |
| 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: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -4.71483 | -36.8459 | -1.47267 |
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 | CD2 | LEU- 545 | 3.65 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 555 | 4.2 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 558 | 4.06 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 558 | 3.81 | 0 | Hydrophobic |
| C6 | CE | MET- 559 | 3.73 | 0 | Hydrophobic |
| C18 | CG | MET- 559 | 3.98 | 0 | Hydrophobic |
| C19 | CE | MET- 559 | 3.52 | 0 | Hydrophobic |
| C19 | CG2 | ILE- 593 | 4.46 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 596 | 4.31 | 0 | Hydrophobic |
| C1 | CG2 | THR- 597 | 4.25 | 0 | Hydrophobic |
| O3 | CZ | ARG- 599 | 3.66 | 0 | Ionic (Protein Cationic) |
| O3 | NH2 | ARG- 599 | 2.91 | 172.66 | H-Bond (Protein Donor) |
| C21 | CG | ARG- 599 | 3.63 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 603 | 4.46 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 603 | 4.09 | 0 | Hydrophobic |
| C22 | CB | TRP- 611 | 4.48 | 0 | Hydrophobic |
| C14 | CZ2 | TRP- 611 | 4.05 | 0 | Hydrophobic |
| C12 | CE2 | TRP- 611 | 4.18 | 0 | Hydrophobic |
| C9 | CZ2 | TRP- 611 | 4.3 | 0 | Hydrophobic |
| C17 | CD2 | TRP- 611 | 4.23 | 0 | Hydrophobic |
| O3 | OG1 | THR- 613 | 3.19 | 151.35 | H-Bond (Protein Donor) |
| C26 | CB | THR- 613 | 3.58 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 615 | 3.64 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 621 | 4.46 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 621 | 3.99 | 0 | Hydrophobic |
| C6 | CE | MET- 625 | 4.11 | 0 | Hydrophobic |
| C5 | CZ | PHE- 626 | 4.26 | 0 | Hydrophobic |
| C4 | CE2 | PHE- 626 | 4.22 | 0 | Hydrophobic |
| O1 | NE2 | GLN- 637 | 2.88 | 156.67 | H-Bond (Protein Donor) |
| C1 | CD1 | PHE- 641 | 4.02 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 724 | 4.25 | 0 | Hydrophobic |
| C4 | CB | ALA- 728 | 4.08 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 731 | 3.47 | 0 | Hydrophobic |
