Identification of a novel fxr ligand that regulates metabolism

Structure

x-ray diffraction · 4 distinct chains · 63% helix, 0% strand (DSSP).

Ligands and binding sites

• IVM · (2ae,4e,5's,6s,6'r,7s,8e,11r,13r,15s,17ar,20r,20ar, 20BS)-6'-[(2S)-butan-2-yl]-20,20B-dihydroxy-5',6,8,19-tetramethyl-17-oxo-3',4',5',6,6',10,11,14,15,17,17A, 20,20A,20B-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacyclooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside · ligand · 2 copies · chains A, B
• FMT · Formic acid · additive · 8 copies · chains B

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

Pockets

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

Interfaces

3 interfaces between chains.

• C–A · 532 Ų buried · 1 hydrogen bond · protein-protein
• D–B · 522 Ų buried · 2 hydrogen bonds · protein-protein
• A–B · 476 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 4WVD · Identification of a novel FXR ligand that regulates metabolism · the same entry in another collection · chain C against C, TM-score 1.00
• O75376 · AlphaFold monomer V2.0 prediction for nuclear receptor corepressor 1 (O75376) · a predicted model of the same protein · chain C against A, TM-score 0.47

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 O75376
• Every structure of UniProt Q96RI1
• Elsewhere: RCSB PDB 4WVD · PDBe 4WVD · UniProt O75376 · UniProt Q96RI1