Crystal structure of mouse CARM1 in complex with inhibitor LH1246

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 37% strand (DSSP).

Ligands and binding sites

• SAO · 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine · ligand · 4 copies · chains A, C, E, G
• LHB · 5-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3, 4-bis(oxidanyl)oxolan-2-yl]methylamino]methyl]-4-azanyl-1-(methoxymethyl)pyrimidin-2-one · ligand · 4 copies · chains B, D, F, H
• M2M · 1-methoxy-2-(2-methoxyethoxy)ethane · ligand · 2 copies · chains C, E
• DXE · 1,2-dimethoxyethane · ligand · chains C
• NA · Sodium ion · metal · 2 copies · chains D, F
• EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D, E, H, F, G
• PG4 · Tetraethylene glycol · additive · 4 copies · chains B, C, D, F
• PEG · Di(hydroxyethyl)ether · additive · chains D

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Interfaces

16 interfaces between chains.

• C–D · 1895 Ų buried · 24 hydrogen bonds · protein-protein
• E–F · 1894 Ų buried · 25 hydrogen bonds · protein-protein
• G–H · 1891 Ų buried · 30 hydrogen bonds · protein-protein
• A–B · 1882 Ų buried · 30 hydrogen bonds · protein-protein
• B–D · 794 Ų buried · 10 hydrogen bonds · protein-protein

Compared structures

• 5LV2 · Crystal structure of mouse CARM1 in complex with inhibitor LH1246 · the same entry in another collection · chain H against H, TM-score 1.00
• Q9WVG6 · AlphaFold monomer V2.0 prediction for histone-arginine methyltransferase CARM1 (Q9WVG6) · a predicted model of the same protein · chain C against A, TM-score 1.00

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 Q9WVG6
• Elsewhere: RCSB PDB 5LV2 · PDBe 5LV2 · UniProt Q9WVG6