Crystal structure of SPINDLIN1 in complex with the methyltransferase inhibitor A366

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 48% strand (DSSP).

Ligands and binding sites

• 2OD · 5'-methoxy-6'-[3-(pyrrolidin-1-yl) propoxy]spiro[cyclobutane-1,3'-indol]-2'-amine · ligand · 2 copies · chains A
• NA · Sodium ion · metal · chains A
• EDO · 1,2-ethanediol · additive · 2 copies · chains A
• DMS · Dimethyl sulfoxide · additive · chains A
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
• GOL · Glycerol · additive · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Compared structures

• 6I8Y · Crystal structure of Spindlin1 in complex with the Methyltransferase inhibitor A366 · the same entry in another collection · chain A against A, TM-score 1.00
• Q9Y657 · AlphaFold monomer V2.0 prediction for spindlin-1 (Q9Y657) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 Q9Y657
• Elsewhere: RCSB PDB 6I8Y · PDBe 6I8Y · UniProt Q9Y657