SMTL ID : 7pjn.2 (1 other biounit)

Crystal Structure of Ivosidenib-resistant IDH1 variant R132C S280F in complex with NADPH and inhibitor DS-1001B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x 7SU: (E)-3-(1-(5-(2-fluoropropan-2-yl)-3-(2,4,6-trichlorophenyl)isoxazole-4-carbonyl)-3-methyl-1H-indol-4-yl)acrylic acid(Non-covalent)

7SU.1: 26 residues within 4Å: Chain A: A.111, I.113, R.119, L.120, V.121, W.124, I.128, I.130, C.132, I.251, V.255, A.258, M.259, W.267, C.269, N.271, V.276, Q.277, S.278, V.281, A.282, S.287, M.291 Chain B: L.120, V.281 Ligands: 7SU.6 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.111, A:L.120, A:W.124, A:W.124, A:I.128, A:I.130, A:I.130, A:W.267, A:V.281 Water bridges: A:A.111, A:A.111, A:I.128 Salt bridges: A:R.119 Halogen bonds: A:V.276 7SU.6: 23 residues within 4Å: Chain A: L.120, V.276, V.281 Chain B: A.111, R.119, L.120, V.121, W.124, I.128, I.130, C.132, I.251, V.255, A.258, M.259, W.267, C.269, S.278, V.281, A.282, S.287, M.291 Ligands: 7SU.1 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.120, B:W.124, B:W.124, B:I.128, B:I.130, B:I.130, B:W.267, B:V.281, B:A.282 Salt bridges: B:R.119

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: M.199, S.202, K.203, V.294, V.296, V.303, R.338, H.342, K.345 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.202 GOL.5: 4 residues within 4Å: Chain A: I.21, Y.316, Y.319, Q.320 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.316, A:Q.320 GOL.7: 8 residues within 4Å: Chain B: M.199, S.202, K.203, V.294, V.296, V.303, R.338, H.342 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.202, B:S.202, B:K.203 GOL.9: 5 residues within 4Å: Chain B: I.5, E.351, F.354, A.412, L.415 No protein-ligand interaction detected (PLIP)

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 5 residues within 4Å: Chain A: T.77, S.94, N.96, R.100 Ligands: NDP.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.77, A:S.94, A:N.96 Salt bridges: A:R.100 CIT.8: 4 residues within 4Å: Chain B: T.77, S.94, N.96 Ligands: NDP.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.77, B:T.77, B:T.77, B:T.77, B:S.94, B:N.96

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

NDP.4: 25 residues within 4Å: Chain A: E.17, K.72, A.74, T.75, I.76, T.77, R.82, N.96, Q.283, L.288, G.289, E.306, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, S.326, T.327, N.328, D.375 Ligands: CIT.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.72, A:T.75, A:T.75, A:T.77, A:R.82, A:R.82, A:N.96, A:E.306, A:G.310, A:T.311, A:V.312, A:N.328, A:N.328 Water bridges: A:R.314, A:A.331 Salt bridges: A:R.314, A:H.315 NDP.10: 26 residues within 4Å: Chain B: E.17, 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, S.326, T.327, N.328, P.329, D.375 Ligands: CIT.8 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:K.72, B:T.75, B:T.77, B:N.96, B:E.306, B:G.310, B:G.310, B:T.311, B:V.312, B:N.328, B:N.328 Salt bridges: B:R.314, B:H.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reinbold, R. et al., Resistance to the isocitrate dehydrogenase 1 mutant inhibitor ivosidenib can be overcome by alternative dimer-interface binding inhibitors. Nat Commun (2022)

Release Date

2022-07-13

Peptides

Isocitrate dehydrogenase [NADP] cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Isocitrate dehydrogenase [NADP] cytoplasmic

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