SMTL ID : 5l57.1

Crystal structure of Iso-citrate Dehydrogenase R132H in complex with a novel inhibitor (compound 13a)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 19 residues within 4Å: Chain A: T.75, I.76, T.77, R.82, N.96, D.279, S.280, L.288, G.289, E.306, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:D.279 Hydrogen bonds: A:T.75, A:T.75, A:T.75, A:T.77, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:H.309, A:G.310, A:G.310, A:T.311, A:V.312, A:T.313, A:N.328 Water bridges: A:A.331 Salt bridges: A:R.314, A:H.315 pi-Stacking: A:H.309 NDP.3: 19 residues within 4Å: Chain B: T.75, I.76, T.77, R.82, N.96, D.279, S.280, L.288, G.289, E.306, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:D.279 Hydrogen bonds: B:T.75, B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:H.309, B:G.310, B:G.310, B:T.311, B:V.312, B:T.313, B:N.328 Water bridges: B:E.306, B:A.331 Salt bridges: B:R.314, B:H.315 pi-Stacking: B:H.309

2 x 6N3: (1~{R},5~{S})-3-[6-(3-methylbutoxy)-5-[[(1~{R},3~{S})-5-oxidanyl-2-adamantyl]carbamoyl]pyridin-2-yl]-3-azabicyclo[3.1.0]hexane-6-carboxylic acid(Non-covalent)

6N3.2: 12 residues within 4Å: Chain A: A.111, R.119, W.124, I.130, H.132, I.251, V.255, W.267, Y.285 Chain B: D.252, M.259 Ligands: 6N3.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.111, A:W.124, A:I.130, A:I.251, A:V.255, A:W.267 Salt bridges: A:R.119 pi-Stacking: A:Y.285 6N3.4: 12 residues within 4Å: Chain A: D.252, M.259 Chain B: A.111, R.119, W.124, I.130, H.132, I.251, V.255, W.267, Y.285 Ligands: 6N3.2 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.111, B:W.124, B:I.130, B:I.251, B:V.255, B:W.267 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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