Crystal structure of rat vdr ligand binding domain in complex with novel nonsecosteroidal ligands

Structure

x-ray diffraction · 2 distinct chains · 65% helix, 3% strand (DSSP).

Ligands and binding sites

• W12 · (2S)-3-{4-[4-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}phenyl)heptan-4-yl]phenoxy}propane-1,2-diol · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–C · 564 Ų buried · 9 hydrogen bonds · protein-protein

Compared structures

• 3W0H · Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel Nonsecosteroidal… · the same entry in another collection · chain A against A, TM-score 1.00
• P13053 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor (P13053) · a predicted model of the same protein · chain A against A, TM-score 0.96
• Q15648 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain C against A, TM-score 0.76

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P13053
• Every structure of UniProt Q15648
• Elsewhere: RCSB PDB 3W0H · PDBe 3W0H · UniProt P13053 · UniProt Q15648