SMTL ID : 8t7o.1

Crystal structure of the R132H mutant of IDH1 bound to AG-120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 18 residues within 4Å: Chain A: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, E.306, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 16 PLIP interactions: 16 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:E.306, A:H.309, A:G.310, A:G.310, A:T.311, A:V.312, A:N.328 Salt bridges: A:R.314, A:H.315 pi-Stacking: A:H.309 NAP.3: 20 residues within 4Å: Chain A: K.260 Chain B: A.74, T.75, I.76, T.77, R.82, N.96, L.288, G.289, A.307, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.72, B:T.75, B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:A.307, B:H.309, B:G.310, B:T.311, B:V.312, B:T.313, B:N.328, B:N.328, A:K.260 Salt bridges: B:R.314, B:H.315, A:K.260

1 x IV3: ivosidenib(Non-covalent)

IV3.2: 18 residues within 4Å: Chain A: L.120, V.255, A.258, M.259, W.267, V.276, Q.277, S.280, V.281 Chain B: L.120, W.124, I.128, I.130, V.255, M.259, W.267, C.269, N.271 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.120, A:L.120, A:V.276, A:V.281, B:L.120, B:W.124, B:W.124 Hydrogen bonds: A:Q.277, A:S.280, A:S.280 Halogen bonds: A:Q.277 pi-Stacking: B:W.267

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

Related Entries With Identical Sequence