Crystal structure of coactivator associated arginine methyltransferase 1 (CARM1) in complex with sinefungin and indole inhibitor

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 37% strand (DSSP).

Ligands and binding sites

• SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
• 845 · N-(3-{5-[5-(1H-indol-4-yl)-1,3,4-oxadiazol-2-yl]-3-(trifluoromethyl)-1H-pyrazol-1-yl}benzyl)-L-alaninamide · ligand · 4 copies · chains A, B, C, D
• CL · Chloride ion · ion · 4 copies · chains A, B, C, D

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• B–D · 1860 Ų buried · 26 hydrogen bonds · protein-protein
• A–C · 1818 Ų buried · 24 hydrogen bonds · protein-protein
• B–C · 677 Ų buried · 8 hydrogen bonds · protein-protein
• A–B · 173 Ų buried · 2 hydrogen bonds · protein-protein
• C–D · 165 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 2Y1X · Crystal structure of coactivator associated arginine methyltransferase 1 (CARM1) in… · the same entry in another collection · chain B against B, TM-score 1.00
• Q86X55 · AlphaFold monomer V2.0 prediction for histone-arginine methyltransferase CARM1 (Q86X55) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 Q86X55
• Elsewhere: RCSB PDB 2Y1X · PDBe 2Y1X · UniProt Q86X55