SMTL ID : 5l58.1

Crystal structure of Iso-citrate Dehydrogenase 1 [IDH1 (R132H)] in complex with a novel inhibitor (Compound 2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.04 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Covalent)

NDP.1: 22 residues within 4Å: Chain A: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, G.289, E.306, A.307, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.72, A:K.72, A:T.75, A:T.77, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:G.310, A:G.310, A:T.311, A:V.312, A:T.313, A:N.328, A:N.328 Salt bridges: A:R.314, A:H.315 NDP.3: 22 residues within 4Å: Chain B: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, G.289, E.306, A.307, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:K.72, B:K.72, B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:G.310, B:G.310, B:T.311, B:V.312, B:T.313, B:N.328, B:N.328 Salt bridges: B:R.314, B:H.315

2 x 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(Non-covalent)

6MX.2: 14 residues within 4Å: Chain A: A.111, R.119, W.124, I.130, I.251, V.255, M.259, W.267, N.271, Y.285 Chain B: D.252, V.255, M.259 Ligands: 6MX.4 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.111, A:W.124, A:W.124, A:I.130, A:I.251, A:V.255, A:W.267, A:Y.285, B:V.255 Hydrogen bonds: A:N.271, A:Y.285 Salt bridges: A:R.119 pi-Stacking: A:Y.285 6MX.4: 14 residues within 4Å: Chain A: D.252, V.255, M.259 Chain B: A.111, R.119, W.124, I.130, I.251, V.255, M.259, W.267, N.271, Y.285 Ligands: 6MX.2 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.111, B:W.124, B:W.124, B:I.130, B:I.251, B:V.255, B:W.267, B:Y.285, A:V.255 Hydrogen bonds: B:N.271, B:Y.285 Salt bridges: B:R.119 pi-Stacking: B:Y.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, S. et al., Discovery and Optimization of Allosteric Inhibitors of Mutant Isocitrate Dehydrogenase 1 (R132H IDH1) Displaying Activity in Human Acute Myeloid Leukemia Cells. J.Med.Chem. (2016)

Release Date

2016-12-14

Peptides

Isocitrate dehydrogenase [NADP] cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Isocitrate dehydrogenase [NADP] cytoplasmic

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