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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: Q.320, K.321, G.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.320 GOL.4: 7 residues within 4Å: Chain A: N.101, I.102, G.104, Y.135, Q.185, K.187, S.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.101 GOL.7: 3 residues within 4Å: Chain B: Q.320, K.321, G.322 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.320 GOL.10: 7 residues within 4Å: Chain B: N.101, I.102, G.104, Y.135, Q.185, K.187, S.188 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.101

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: R.109, D.275, D.279 Chain B: D.252 Ligands: AKG.3 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.275, A:D.279, B:D.252, H2O.2, H2O.4 CA.8: 5 residues within 4Å: Chain A: D.252 Chain B: R.109, D.275, D.279 Ligands: AKG.9 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.7, H2O.9

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

AKG.3: 14 residues within 4Å: Chain A: T.77, S.94, N.96, R.100, R.109, Y.139, D.275, A.308 Chain B: K.212, T.214, I.215, D.252 Ligands: CA.2, NDP.5 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.77, A:S.94, A:N.96, A:Y.139, B:K.212 Salt bridges: A:R.100, A:R.109 Water bridges: B:T.214 AKG.9: 14 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, A.308 Ligands: CA.8, NDP.11 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:K.212, B:T.77, B:S.94, B:N.96, B:Y.139 Water bridges: A:T.214 Salt bridges: B:R.100, B:R.109

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

NDP.5: 29 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, T.327, N.328, D.375 Chain B: T.214, L.250, D.252, D.253, Q.257, K.260 Ligands: AKG.3 30 PLIP interactions: 24 interactions with chain A, 6 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:R.82, A:R.82, A:N.96, A:G.310, A:G.310, A:T.311, A:V.312, A:R.314, A:R.314, A:N.328, A:N.328, B:D.253, B:Q.257 Water bridges: A:T.313, A:R.314, A:H.315, A:H.315, A:H.315, B:D.253, B:D.253, B:K.260 Salt bridges: A:R.314, A:H.315, B:K.260 NDP.11: 29 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, L.288, G.289, A.307, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 Ligands: AKG.9 30 PLIP interactions: 24 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:K.72, B:T.75, B:T.75, B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:G.310, B:G.310, B:T.311, B:V.312, B:R.314, B:R.314, B:N.328, B:N.328, A:Q.257 Water bridges: B:T.313, B:R.314, B:H.315, B:H.315, B:H.315, A:D.253, A:D.253, A:D.253, A:K.260 Salt bridges: B:R.314, B:H.315, A:K.260

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

CL.6: 4 residues within 4Å: Chain A: L.103, C.297, P.298, D.299 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: L.103, C.297, P.298, 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
C

B
C

Isocitrate dehydrogenase [NADP] cytoplasmic

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