SMTL ID : 9b81.1

Crystal structure of wild type IDH1 bound to compound 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-dimer

Ligands

2 x 01: 2-methyl-2-(6-{4-[(2S)-1,1,1-trifluoro-2-hydroxypropan-2-yl]benzoyl}-6,11-dihydro-5H-pyrido[2,3-b][1,5]benzodiazepin-8-yl)propanenitrile

01.1: 12 residues within 4Å: Chain A: R.109, A.111, I.113, L.120, W.124, P.127, I.128, I.130, H.132, V.255, W.267, M.291 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.111, A:I.113, A:W.124, A:W.124, A:I.130, A:W.267 Hydrogen bonds: A:I.128, A:I.128 pi-Stacking: A:W.124 01.4: 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, H.132, V.255, W.267, M.291 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.111, B:I.113, B:R.119, B:L.120, B:W.124, B:W.124, B:W.124, B:I.130, B:W.267 Hydrogen bonds: B:I.128, B:I.128 pi-Stacking: B:W.124

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

NAP.2: 20 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, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:K.72, 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:G.310, A:G.310, A:T.311, A:V.312, A:T.313, A:T.313, A:N.328, A:N.328 Water bridges: A:R.314 Salt bridges: A:H.315 pi-Stacking: A:H.309 NAP.5: 20 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, 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 B Hydrogen bonds: B:T.75, 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:G.310, B:T.311, B:V.312, B:N.328, B:N.328 Salt bridges: B:R.314, B:H.315 pi-Stacking: B:H.309

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: K.350, E.351, F.354, A.412 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.350

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

2025-03-26

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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