SMTL ID : 4xrx.1

Crystal structure of a metabolic reductase with (E)-5-((1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl)pyridin-2(1H)-one

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 22 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 Chain B: K.260 Ligands: 42V.2 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.72, A:T.75, A:T.75, A:T.77, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:G.310, A:G.310, A:T.311, A:V.312, A:N.328, A:N.328 Salt bridges: A:R.314, A:H.315, B:K.260 NDP.3: 21 residues within 4Å: Chain A: K.260 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 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.72, B:T.75, B:T.75, B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, 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, A:K.260 pi-Stacking: B:H.309

1 x 42V: 5-[(E)-(1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl]pyridin-2(1H)-one(Non-covalent)

42V.2: 8 residues within 4Å: Chain A: T.77, S.94, N.96, G.97, R.100, N.101, R.140 Ligands: NDP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.94, A:R.100, A:R.100, A:N.101, A:R.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, F. et al., Inhibition of Cancer-Associated Mutant Isocitrate Dehydrogenases by 2-Thiohydantoin Compounds. J.Med.Chem. (2015)

Release Date

2015-12-09

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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