Crystal structure of human mitochondrial isocitrate dehydrogenase (IDH2) R140Q mutant homodimer in complex with ag-221 (enasidenib) inhibitor.

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 21% strand (DSSP).

Ligands and binding sites

• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
• 69Q · 2-methyl-1-[(4-[6-(trifluoromethyl)pyridin-2-yl]-6-{[2-(trifluoromethyl)pyridin-4-yl]amino}-1,3,5-triazin-2-yl)amino]propan-2-ol · ligand · chains A, B
• CA · Calcium ion · metal · 2 copies · chains A, B
• NA · Sodium ion · metal · 2 copies · chains A, B
• GOL · Glycerol · additive · 5 copies · chains A, B
• ACT · Acetate ion · additive · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 3063 Ų buried · 50 hydrogen bonds · protein-protein

Compared structures

• 5I96 · Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant… · the same entry in another collection · chain A against A, TM-score 1.00
• P48735 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP], mitochondrial… · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P48735
• Elsewhere: RCSB PDB 5I96 · PDBe 5I96 · UniProt P48735