SMTL ID : 6o2z.1

Crystal structure of IDH1 R132H mutant in complex with compound 32

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x LJV: 6-{[(6-chloro-2-oxo-1,2-dihydroquinolin-3-yl)methyl]amino}-2-methylpyridine-3-carbonitrile(Non-covalent)

LJV.1: 17 residues within 4Å: Chain A: R.109, A.111, I.113, R.119, L.120, W.124, I.128, I.130, A.258, M.259, W.267, D.279, V.281, A.282, Y.285, M.291 Chain B: S.280 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.111, A:I.113, A:I.128, A:I.130, A:I.130, A:V.281, A:V.281, A:V.281, A:Y.285 Hydrogen bonds: A:R.109, A:A.111, A:L.120, A:I.128, A:D.279 Water bridges: A:I.128, A:I.128 LJV.4: 17 residues within 4Å: Chain A: S.280 Chain B: R.109, A.111, I.113, R.119, L.120, W.124, I.128, I.130, A.258, M.259, W.267, D.279, V.281, A.282, Y.285, M.291 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:A.111, B:I.113, B:W.124, B:I.128, B:I.130, B:V.281, B:V.281, B:V.281, B:Y.285 Hydrogen bonds: B:A.111, B:L.120, B:I.128, B:D.279 Water bridges: B:I.128, B:I.128 pi-Stacking: B:W.267

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 19 residues within 4Å: Chain A: K.72, A.74, T.75, I.76, T.77, R.82, N.96, Q.277, 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 A Hydrogen bonds: A:K.72, A:T.75, A:T.75, A:T.77, A:T.77, A:T.77, A:R.82, A:R.82, A:H.309, A:G.310, A:G.310, A:T.311, A:V.312, A:T.313, A:N.328 Water bridges: A:T.313, A:R.314, A:A.331 Salt bridges: A:R.314, A:H.315 NAP.5: 21 residues within 4Å: Chain B: K.72, A.74, T.75, I.76, T.77, R.82, N.96, Q.277, S.287, G.289, E.306, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:K.72, B:K.72, B:T.75, B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:E.306, 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 pi-Stacking: B:H.309

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: S.6, G.7, G.8, E.36, D.38 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.7, A:G.8 GOL.6: 5 residues within 4Å: Chain B: S.6, G.7, G.8, E.36, D.38 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.7, B:G.8, B:E.36, B:D.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, J. et al., Discovery and Optimization of Quinolinone Derivatives as Potent, Selective, and Orally Bioavailable Mutant Isocitrate Dehydrogenase 1 (mIDH1) Inhibitors. J.Med.Chem. (2019)

Release Date

2019-06-26

Peptides

Isocitrate dehydrogenase [NADP] cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isocitrate dehydrogenase [NADP] cytoplasmic

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