SMTL ID : 4i3k.1

Crystal structure of a metabolic reductase with 1-hydroxy-6-(4-hydroxybenzyl)-4-methylpyridin-2(1H)-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.31 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 18 residues within 4Å: Chain A: K.72, A.74, T.75, 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: 1BX.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:K.72, 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:H.309, A:G.310, A:T.311, A:V.312, A:N.328 Salt bridges: A:R.314, A:H.315 NDP.6: 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, S.326, T.327, N.328 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:K.72, 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:H.309, B:G.310, B:G.310, B:T.311, B:V.312, B:T.313, B:T.313, B:N.328 Salt bridges: B:R.314, B:H.315

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: M.318, K.374 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.314, A:K.374 SO4.3: 2 residues within 4Å: Chain A: T.313, R.317 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.317 SO4.4: 7 residues within 4Å: Chain A: H.170, N.171, F.172, E.173, E.174, G.175 Chain B: Q.185 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.173, A:E.174, A:G.175, B:Q.185 Salt bridges: A:H.170 SO4.7: 3 residues within 4Å: Chain B: R.82, T.313, R.317 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.82, B:R.317

1 x 1BX: 1-hydroxy-6-(4-hydroxybenzyl)-4-methylpyridin-2(1H)-one(Non-covalent)

1BX.5: 5 residues within 4Å: Chain A: T.77, S.94, N.96, R.100 Ligands: NDP.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.77 Hydrogen bonds: A:R.100, A:R.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, B. et al., Crystallographic Investigation and Selective Inhibition of Mutant Isocitrate Dehydrogenase. ACS Med Chem Lett (2013)

Release Date

2013-05-22

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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