The crystal structure of human HMT1 hnrnp methyltransferase-like protein 6 in complex with compound ds-421 (2-{4-[3-chloro-2-(2- methoxyphenyl)-1H-indol-5-YL]PIPERIDIN-1-yl}-N-methylethanamine

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 35% strand (DSSP).

Ligands and binding sites

• SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, B, C
• 36S · 2-{4-[3-chloro-2-(2-methoxyphenyl)-1H-indol-5-yl]piperidin-1-yl}-N-methylethanamine · ligand · 3 copies · chains A, B, C

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

Pockets

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

Interfaces

5 interfaces between chains.

• A–B · 370 Ų buried · 7 hydrogen bonds · protein-protein
• B–E · 265 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 259 Ų buried · 8 hydrogen bonds · protein-protein
• C–F · 249 Ų buried · 2 hydrogen bonds · protein-protein
• A–D · 99 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 4QPP · The Crystal Structure of Human HMT1 hnRNP methyltransferase-like protein 6 in complex… · the same entry in another collection · chain F against F, TM-score 1.00
• Q96LA8 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 6 (Q96LA8) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q96LA8
• Elsewhere: RCSB PDB 4QPP · PDBe 4QPP · UniProt Q96LA8