Crystal structure of the human ppar-alpha ligand-binding domain in complex with an antagonist GW6471 and a smrt corepressor motif

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 4% strand (DSSP).

Ligands and binding sites

• 471 · N-((2S)-2-({(1Z)-1-methyl-3-oxo-3-[4-(trifluoromethyl) phenyl]prop-1-enyl}amino)-3-{4-[2-(5-methyl-2-phenyl-1,3-oxazol-4-yl)ethoxy]phenyl}propyl)propanamide · ligand · 4 copies · chains A, B, F, C, D

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

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

10 interfaces between chains.

• A–E · 1013 Ų buried · 5 hydrogen bonds · protein-protein
• B–F · 936 Ų buried · 4 hydrogen bonds · protein-protein
• D–H · 912 Ų buried · 5 hydrogen bonds · protein-protein
• C–G · 841 Ų buried · 4 hydrogen bonds · protein-protein
• B–D · 465 Ų buried · 7 hydrogen bonds · protein-protein

Compared structures

• 1KKQ · Crystal structure of the human PPAR-alpha ligand-binding domain in complex with an… · the same entry in another collection · chain H against H, TM-score 1.00
• Q07869 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor alpha… · a predicted model of the same protein · chain A against A, TM-score 0.92
• Q9Y618 · AlphaFold monomer V2.0 prediction for nuclear receptor corepressor 2 (Q9Y618) · a predicted model of the same protein · chain E against A, TM-score 0.33

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 Q07869
• Every structure of UniProt Q9Y618
• Elsewhere: RCSB PDB 1KKQ · PDBe 1KKQ · UniProt Q07869 · UniProt Q9Y618