SMTL ID : 8hb9.2 (2 other biounits)

Crystal Structure of Human IDH1 R132H Mutant in Complex with NADPH and Compound IHMT-IDH1-053

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x R1R: [2-[2-[[1-[4-[(1S)-1-[[5-fluoranyl-4-[(4S)-2-oxidanylidene-4-propan-2-yl-1,3-oxazolidin-3-yl]pyrimidin-2-yl]amino]ethyl]phenyl]piperidin-4-yl]sulfamoyl]ethylsulfanylmethyl]-3-oxidanylidene-propyl]-trimethyl-azanium(Covalent)

R1R.1: 19 residues within 4Å: Chain A: R.109, A.111, I.113, R.119, L.120, W.124, P.127, I.128, I.130, H.132, W.267, C.269, N.271, V.281, A.282, Y.285, S.287, M.291 Ligands: PEG.14 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.130, A:I.130, A:I.130, A:W.267, A:V.281, A:A.282 Hydrogen bonds: A:A.111, A:L.120, A:I.128, A:I.128, A:N.271 pi-Stacking: A:W.124 R1R.11: 19 residues within 4Å: Chain B: R.109, A.111, I.113, R.119, L.120, W.124, P.127, I.128, I.130, H.132, W.267, C.269, N.271, V.281, A.282, Y.285, S.287, M.291 Ligands: PEG.14 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.130, B:W.267, B:V.281, B:A.282 Hydrogen bonds: B:A.111, B:L.120, B:I.128, B:I.128 pi-Stacking: B:W.124

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

NDP.2: 19 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, 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.77, A:T.77, A:R.82, A:R.82, A:N.96, A:E.306, A:G.310, A:G.310, A:T.311, A:V.312, A:N.328, A:N.328 Water bridges: A:Q.283, A:E.306, A:E.306, A:A.331 Salt bridges: A:R.314, A:H.315 NDP.12: 19 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, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:K.72, B:T.75, B:T.77, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:E.306, B:G.310, B:T.311, B:V.312, B:N.328, B:N.328 Salt bridges: B:R.314, B:H.315

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: K.65, I.102, L.103, C.297, P.298, D.299, T.302 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.102, A:D.299, A:D.299 GOL.4: 5 residues within 4Å: Chain A: K.345, N.348, N.349, K.350, A.353 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.348 GOL.7: 3 residues within 4Å: Chain A: D.191, H.194, P.298 No protein-ligand interaction detected (PLIP) GOL.8: 2 residues within 4Å: Chain A: Q.320, K.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.320 Water bridges: A:Q.320 GOL.13: 2 residues within 4Å: Chain B: K.4, E.351 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.351

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 7 residues within 4Å: Chain A: M.199, S.202, V.296, G.300, R.338, H.342, K.345 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.202, A:G.300 PEG.6: 5 residues within 4Å: Chain A: S.6, G.7, G.8, E.36, D.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.8 PEG.9: 5 residues within 4Å: Chain A: E.190, R.222, E.229, I.230, K.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.222, A:R.222 PEG.10: 3 residues within 4Å: Chain A: L.201, S.202, K.345 No protein-ligand interaction detected (PLIP) PEG.14: 2 residues within 4Å: Ligands: R1R.1, R1R.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liang, Q. et al., Structure-based discovery of IHMT-IDH1-053 as a potent irreversible IDH1 mutant selective inhibitor. Eur.J.Med.Chem. (2023)

Release Date

2023-05-24

Peptides

Isocitrate dehydrogenase [NADP] cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
DDD

Isocitrate dehydrogenase [NADP] cytoplasmic

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