SMTL ID : 8t7n.1

Crystal structure of the R132H mutant of IDH1 bound to compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 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 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.75, A:T.77, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:E.306, A:H.309, A:G.310, A:G.310, A:T.311, A:V.312, A:N.328 Water bridges: A:A.331 Salt bridges: A:R.314, A:H.315 NAP.3: 21 residues within 4Å: Chain B: 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 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:E.306, B:G.310, B:T.311, B:V.312, B:T.313, B:N.328, B:N.328 Water bridges: B:T.75, B:A.331 Salt bridges: B:R.314, B:H.315 pi-Stacking: B:H.309

2 x ZT3: N-(4-tert-butylphenyl)-7,8-dimethyl-5,11-dihydro-6H-pyrido[2,3-b][1,5]benzodiazepine-6-carboxamide(Non-covalent)

ZT3.2: 12 residues within 4Å: Chain A: R.109, A.111, I.113, L.120, W.124, P.127, I.128, I.130, V.255, M.259, W.267, M.291 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.109, A:A.111, A:I.113, A:I.130, A:V.255, A:V.255, A:W.267 Hydrogen bonds: A:I.128, A:I.128 pi-Stacking: A:W.124 ZT3.4: 14 residues within 4Å: Chain B: R.109, A.111, I.113, R.119, L.120, W.124, K.126, P.127, I.128, I.130, V.255, M.259, W.267, M.291 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:R.109, B:A.111, B:I.113, B:R.119, B:L.120, B:I.130, B:I.130, B:V.255, B:V.255, B:W.267 Hydrogen bonds: B:I.128, B:I.128 pi-Stacking: B:W.124, B:W.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCoy, M.A. et al., Biostructural, biochemical and biophysical studies of mutant IDH1. Nat Commun (2024)

Release Date

2024-08-28

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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