Crystal structure of iso-citrate dehydrogenase 1 [IDH1 (R132H)] in complex with a novel inhibitor (compound 2)

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 20% strand (DSSP).

Ligands and binding sites

• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
• 6MX · 2-[(3~{R})-1-[6-cyclohexylsulfanyl-5-[[(1~{R},3~{S})-5-oxidanyl-2-adamantyl]carbamoyl]pyridin-2-yl]pyrrolidin-3-yl]ethanoic acid · ligand · chains A

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 5L58 · Crystal structure of Iso-citrate Dehydrogenase 1 [IDH1 (R132H)] in complex with a novel… · the same entry in another collection · chain A against A, TM-score 1.00
• O75874 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] cytoplasmic (O75874) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 O75874
• Elsewhere: RCSB PDB 5L58 · PDBe 5L58 · UniProt O75874