SMTL ID : 4xs3.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.29 Å

Oligo State

homo-dimer

Ligands

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

42W.1: 8 residues within 4Å: Chain A: T.77, K.93, S.94, G.97, R.100, N.101, R.109 Ligands: NAP.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.93 Hydrogen bonds: A:S.94, A:S.94, A:N.101, A:R.109 42W.3: 8 residues within 4Å: Chain B: T.77, W.92, K.93, S.94, N.96, G.97, R.100 Ligands: NAP.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.77, B:K.93 Hydrogen bonds: B:S.94, B:S.94, B:R.100, B:R.100

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

NAP.2: 15 residues within 4Å: Chain A: T.75, T.77, R.82, L.288, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315 Chain B: A.256, K.260 Ligands: 42W.1 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.77, A:T.77, A:R.82, A:R.82, A:G.310, A:T.311, A:V.312, A:T.313, B:A.256 Salt bridges: A:R.314, A:H.315 NAP.4: 21 residues within 4Å: Chain A: K.260 Chain B: K.72, C.73, A.74, T.75, I.76, T.77, R.82, N.96, G.289, E.306, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 Ligands: 42W.3 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:A.74 Hydrogen bonds: B:K.72, B:K.72, B:T.75, B:T.77, 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 pi-Stacking: B:H.309

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

2016-07-27

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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