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

Crystal Structure of human IDH1 mutant (R132H) in complex with NADP+ and an Inhibitor related to BAY 1436032

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 21 residues within 4Å: Chain A: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, G.289, E.306, A.307, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.72, A:T.75, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:H.309, A:H.309, A:G.310, A:G.310, A:T.311, A:V.312, A:N.328 Water bridges: A:R.314, A:H.315, A:A.331 Salt bridges: A:R.314, A:H.315 NAP.4: 21 residues within 4Å: Chain B: K.72, A.74, T.75, I.76, T.77, R.82, N.96, Q.277, L.288, G.289, E.306, A.307, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Q.277 Hydrogen bonds: B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:Q.277, B:H.309, B:G.310, B:T.311, B:V.312, B:T.313, B:N.328, B:N.328 Water bridges: B:D.279, B:D.279, B:H.315 Salt bridges: B:R.314, B:H.315

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: A.369, G.370 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.370, A:S.389 EDO.3: 1 residues within 4Å: Chain A: W.245 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 3 residues within 4Å: Chain B: D.50, A.51, K.89 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.50, B:D.50

1 x 6VN: 2-[(4-propan-2-ylphenyl)amino]-1-[(1~{S},5~{S})-3,3,5-trimethylcyclohexyl]benzimidazole-5-carboxylic acid(Non-covalent)

6VN.6: 17 residues within 4Å: Chain A: L.120, A.258, M.259, V.276, Q.277, S.280, V.281 Chain B: W.124, I.128, I.130, H.132, M.259, C.269, S.280, V.281, G.284, Y.285 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.120, A:A.258, A:V.276, A:Q.277, A:V.281, B:W.124, B:I.128, B:Y.285 Hydrogen bonds: A:Q.277, B:N.271, B:S.280 Salt bridges: B:H.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pusch, S. et al., Pan-mutant IDH1 inhibitor BAY 1436032 for effective treatment of IDH1 mutant astrocytoma in vivo. Acta Neuropathol. (2017)

Release Date

2017-02-08

Peptides

Isocitrate dehydrogenase [NADP] cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Isocitrate dehydrogenase [NADP] cytoplasmic

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