SMTL ID : 6b0z.2 (1 other biounit)

IDH1 R132H mutant in complex with IDH305

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 23 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, E.309, 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.3 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: 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:T.78, A:E.309, A:A.334 Salt bridges: A:R.317, A:H.318, B:K.263 NDP.4: 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.6 18 PLIP interactions: 1 interactions with chain A, 17 interactions with chain B Water bridges: A:K.263, B:G.292, B:A.334 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:H.312, B:G.313, B:T.314, B:V.315, B:N.331 Salt bridges: B:R.317, B:H.318

3 x C81: (4R)-4-[(1S)-1-fluoroethyl]-3-[2-({(1S)-1-[4-methyl-2'-(trifluoromethyl)[3,4'-bipyridin]-6-yl]ethyl}amino)pyrimidin-4-yl]-1,3-oxazolidin-2-one(Non-covalent)

C81.2: 20 residues within 4Å: Chain A: R.112, E.113, A.114, I.116, R.122, L.123, W.127, I.131, I.133, V.258, M.262, W.270, Y.275, Q.280, S.281, V.284, Y.288, S.290, M.294 Ligands: C81.7 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:R.112, A:A.114, A:I.116, A:W.127, A:I.131, A:I.131, A:I.133, A:W.270, A:V.284 Hydrogen bonds: A:A.114, A:L.123, A:I.131, A:I.131 Water bridges: A:S.290 Halogen bonds: A:V.258 C81.5: 20 residues within 4Å: Chain A: V.284 Chain B: R.112, E.113, A.114, I.116, R.122, L.123, W.127, P.130, I.131, I.133, V.258, M.262, S.281, V.284, A.285, Y.288, S.290, M.294 Ligands: C81.7 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.116, B:W.127, B:W.127, B:I.131, B:I.131, B:I.133, B:A.285 Hydrogen bonds: B:A.114, B:L.123, B:I.131, B:I.131 Halogen bonds: B:V.258 C81.7: 16 residues within 4Å: Chain A: L.123, V.279, Q.280, V.284 Chain B: L.123, I.133, H.135, I.254, V.258, W.270, C.272, Q.280, S.281, V.284 Ligands: C81.2, C81.5 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.279, A:V.284, B:V.258, B:V.284 Hydrogen bonds: A:Q.280

2 x FLC: CITRATE ANION(Non-covalent)

FLC.3: 5 residues within 4Å: Chain A: T.80, S.97, N.99, R.103 Ligands: NDP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.80, A:T.80, A:S.97, A:N.99 Salt bridges: A:R.103 FLC.6: 4 residues within 4Å: Chain B: T.80, S.97, N.99 Ligands: NDP.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.97, B:N.99 Salt bridges: B:R.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cho, Y.S. et al., Discovery and Evaluation of Clinical Candidate IDH305, a Brain Penetrant Mutant IDH1 Inhibitor. ACS Med Chem Lett (2017)

Release Date

2017-11-08

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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