SMTL ID : 5tqh.2 (1 other biounit)

IDH1 R132H mutant in complex with IDH889

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x 7J2: (4S)-3-[2-({(1S)-1-[5-(4-fluoro-3-methylphenyl)pyrimidin-2-yl]ethyl}amino)pyrimidin-4-yl]-4-(propan-2-yl)-1,3-oxazolidin-2-one(Non-covalent)

7J2.1: 20 residues within 4Å: Chain A: R.112, E.113, A.114, I.116, R.122, L.123, W.127, P.130, I.131, I.133, V.258, M.262, W.270, Y.275, Q.280, S.281, V.284, Y.288, S.290, M.294 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.112, A:W.127, A:W.127, A:W.127, A:W.270, A:W.270, A:V.284 Hydrogen bonds: A:A.114, A:L.123, A:I.131, A:I.131 7J2.4: 19 residues within 4Å: Chain A: V.284 Chain B: R.112, A.114, I.116, R.122, L.123, W.127, P.130, I.131, I.133, A.261, M.262, W.270, S.281, V.284, A.285, Y.288, S.290, M.294 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.116, B:W.127, B:W.127, B:I.133, B:A.261, B:W.270, B:V.284, B:A.285 Hydrogen bonds: B:A.114, B:L.123, B:I.131, B:I.131

2 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 6 residues within 4Å: Chain A: T.80, S.97, N.99, R.103, D.278 Ligands: NDP.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.80, A:S.97, A:N.99 Water bridges: A:G.100, A:G.100 Salt bridges: A:R.103 FLC.5: 5 residues within 4Å: Chain B: T.80, S.97, N.99, R.103 Ligands: NDP.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.97, B:N.99 Salt bridges: B:R.103

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

NDP.3: 22 residues within 4Å: Chain A: K.75, A.77, T.78, I.79, T.80, R.85, N.99, Q.286, L.291, G.292, H.312, G.313, T.314, V.315, T.316, R.317, H.318, T.330, N.331, D.378 Chain B: K.263 Ligands: FLC.2 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.78, A:T.78, A:T.80, A:T.80, A:R.85, A:R.85, A:N.99, A:E.309, A:G.313, A:T.314, A:V.315, A:N.331, A:N.331 Water bridges: A:Q.286, A:E.309, A:T.316, A:H.318, A:A.334 Salt bridges: A:R.317, A:H.318, B:K.263 NDP.6: 20 residues within 4Å: Chain B: K.75, A.77, T.78, I.79, T.80, R.85, N.99, L.291, G.292, E.309, H.312, G.313, T.314, V.315, T.316, R.317, H.318, T.330, N.331 Ligands: FLC.5 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:T.78, B:T.80, B:T.80, B:T.80, B:R.85, B:R.85, B:N.99, B:E.309, B:G.313, B:T.314, B:V.315, B:N.331, B:N.331 Water bridges: B:G.292, B:A.334 Salt bridges: B:R.317, B:H.318

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Levell, J.R. et al., Optimization of 3-Pyrimidin-4-yl-oxazolidin-2-ones as Allosteric and Mutant Specific Inhibitors of IDH1. ACS Med Chem Lett (2017)

Release Date

2017-01-25

Peptides

Isocitrate dehydrogenase [NADP] cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Isocitrate dehydrogenase [NADP] cytoplasmic

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