Structure-activity relationship study of vitamin D analogs with oxolane group in their side chain

Structure

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

Ligands and binding sites

• 9CW · (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{A}~{S}, 7~{A}~{R})-7~{A}-methyl-1-[(1~{S})-1-[(2~{S},5~{S})-5-(2-oxidanylpropan-2-yl)oxolan-2-yl]ethyl]-2,3,3~{A},5, 6,7-hexahydro-1~{H}-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

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

Interfaces

1 interface between chains.

• A–B · 625 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 5NMA · Structure-activity relationship study of vitamin D analogs with oxolane group in their… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9PTN2 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor a (Q9PTN2) · 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 Q9PTN2
• Every structure of UniProt Q15788
• Elsewhere: RCSB PDB 5NMA · PDBe 5NMA · UniProt Q9PTN2 · UniProt Q15788