A new class of vitamin D receptor ligands that induce structural rearrangement of the ligand-binding pocket

Structure

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

Ligands and binding sites

• JB1 · (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-(2-hydroxyethyl)heptan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol · ligand · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–C · 548 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 2ZXM · A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the… · 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 0.98
• A1L0Z0 · 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 0.55

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 A1L0Z0
• Elsewhere: RCSB PDB 2ZXM · PDBe 2ZXM · UniProt P13053 · UniProt A1L0Z0