SMTL ID : 7pjm.1 (1 other biounit)

Crystal Structure of Ivosidenib-resistant IDH1 variant R132C S280F in complex with NADPH and Ca2+/2-Oxoglutarate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.1: 13 residues within 4Å: Chain A: T.77, S.94, N.96, R.100, R.109, Y.139, D.275 Chain B: K.212, T.214, I.215, D.252 Ligands: NDP.4, CA.5 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.94, A:N.96, B:K.212 Water bridges: A:T.77, A:T.77, B:T.214 Salt bridges: A:R.100, A:R.109 AKG.8: 13 residues within 4Å: Chain A: K.212, T.214, I.215, D.252 Chain B: T.77, S.94, N.96, R.100, R.109, Y.139, D.275 Ligands: CA.7, NDP.9 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:T.77, B:S.94, B:N.96, A:K.212 Salt bridges: B:R.100, B:R.109, A:K.212 Water bridges: A:T.214, A:D.252, A:D.252

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.249, D.253, Q.257 Chain B: R.314 Ligands: NDP.9 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.249, A:D.253 Water bridges: B:R.314 GOL.3: 6 residues within 4Å: Chain A: S.6, G.7, G.8, E.36, L.37, D.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.6, A:G.8, A:E.36

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

NDP.4: 30 residues within 4Å: Chain A: E.17, K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, G.289, A.307, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, S.326, T.327, N.328, D.375 Chain B: T.214, L.250, D.252, D.253, Q.257, K.260 Ligands: AKG.1 28 PLIP interactions: 24 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.72, 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:G.310, A:T.311, A:V.312, A:R.314, A:N.328, A:N.328, B:Q.257 Water bridges: A:T.313, A:R.314, A:H.315, A:H.315, A:A.331, B:D.253, B:K.260 Salt bridges: A:R.314, A:H.315, B:K.260 pi-Stacking: A:H.309 NDP.9: 30 residues within 4Å: Chain A: T.214, L.250, D.252, D.253, Q.257, K.260 Chain B: E.17, K.72, A.74, T.75, I.76, T.77, R.82, N.96, R.100, L.288, G.289, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 Ligands: GOL.2, AKG.8 23 PLIP interactions: 3 interactions with chain A, 20 interactions with chain B Hydrogen bonds: A:D.253, A:Q.257, B:K.72, B:T.75, B:T.75, B:T.77, B:R.82, B:R.82, B:N.96, B:G.310, B:T.311, B:V.312, B:N.328, B:N.328 Salt bridges: A:K.260, B:R.314, B:H.315 Water bridges: B:T.313, B:R.314, B:H.315, B:H.315, B:A.331 pi-Stacking: B:H.309

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: R.109, D.275, D.279 Chain B: D.252 Ligands: AKG.1 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.275, A:D.275, B:D.252, H2O.3, H2O.4 CA.7: 5 residues within 4Å: Chain A: D.252 Chain B: R.109, D.275, D.279 Ligands: AKG.8 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.275, B:D.279, A:D.252, H2O.6, H2O.7

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 5 residues within 4Å: Chain A: L.103, C.297, P.298, D.299, T.302 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: L.103, C.297, D.299 Ligand excluded by PLIP

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
A

B
B

Isocitrate dehydrogenase [NADP] cytoplasmic

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