SMTL ID : 6bky.3 (2 other biounits)

Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with Cmpd2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.252 Chain B: D.275, D.279 Ligands: LMR.3 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.252, B:D.275, H2O.4, H2O.8

1 x K32: 4,5,6,7-TETRABROMO-1H,3H-BENZIMIDAZOL-2-ONE(Non-covalent)

K32.2: 14 residues within 4Å: Chain A: V.121, W.124, V.255, M.259, Q.277, S.280, V.281 Chain B: V.121, W.124, V.255, M.259, Q.277, S.280, V.281 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.277, B:Q.277, B:S.280, A:Q.277, A:Q.277, A:S.280

1 x LMR: (2S)-2-hydroxybutanedioic acid(Non-covalent)

LMR.3: 12 residues within 4Å: Chain A: K.212, I.215, D.252 Chain B: T.77, S.94, N.96, R.100, R.109, R.132, Y.139, D.275 Ligands: MG.1 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.77, B:S.94, B:N.96, B:R.100, B:R.132, B:R.132 Water bridges: B:R.109, B:R.109 Salt bridges: B:R.100, B:R.109, B:R.132, A:K.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jakob, C.G. et al., Novel Modes of Inhibition of Wild-Type Isocitrate Dehydrogenase 1 (IDH1): Direct Covalent Modification of His315. J. Med. Chem. (2018)

Release Date

2018-07-25

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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