Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK3

Structure

x-ray diffraction · 2 distinct chains · 67% helix, 3% strand (DSSP).

Ligands and binding sites

• TK3 · (1R,3R,7E,17beta)-17-{(2R,6R)-6-hydroxy-7-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hept-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol · ligand · chains A
• EDO · 1,2-ethanediol · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 581 Ų buried · 9 hydrogen bonds · protein-protein

Compared structures

• 3VTC · Crystal structure of rat vitamin D receptor bound to a partial agonist… · 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

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
• Elsewhere: RCSB PDB 3VTC · PDBe 3VTC · UniProt P13053