SMTL ID : 6bl0.1 (1 other biounit)

Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of His315 with Cmpd11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.275, D.279 Chain B: D.252 Ligands: ICT.2 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.252, A:D.275, H2O.1, H2O.6 MG.3: 3 residues within 4Å: Chain A: D.252 Chain B: D.275 Ligands: ICT.5 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.2, H2O.6

2 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.2: 12 residues within 4Å: Chain A: T.77, S.94, N.96, R.100, R.109, R.132, Y.139, D.275 Chain B: K.212, I.215, D.252 Ligands: MG.1 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.94, A:N.96, A:D.275, B:K.212 Water bridges: A:R.100, A:R.109, A:R.109 Salt bridges: A:R.100, A:R.100, A:R.109, A:R.132, A:R.132, B:K.212 ICT.5: 14 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, A.308 Ligands: MG.3, NAP.6 12 PLIP interactions: 2 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:K.212, B:T.77, B:S.94, B:N.96 Salt bridges: A:K.212, B:R.100, B:R.100, B:R.109, B:R.132, B:R.132 Water bridges: B:R.100, B:R.109

1 x DWJ: (5aS,6S,8S,9aS)-2-(benzenecarbonyl)-6-methyl-7-oxo-9a-phenyl-4,5,5a,6,7,8,9,9a-octahydro-2H-benzo[g]indazole-8-carbonitrile(Covalent)

DWJ.4: 14 residues within 4Å: Chain A: G.289, H.309, V.312, R.314, H.315, M.318, E.324, T.325, S.326, T.327, N.328, K.374, D.375, L.383 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.309, A:V.312, A:V.312, A:R.314, A:N.328, A:K.374, A:K.374, A:L.383 Hydrogen bonds: A:S.326, A:N.328 pi-Stacking: A:H.309

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

NAP.6: 25 residues within 4Å: Chain A: L.250, D.253, Q.257, K.260 Chain B: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, G.289, E.306, A.307, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 Ligands: ICT.5 28 PLIP interactions: 20 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:E.306, B:G.310, B:G.310, B:T.311, B:V.312, B:N.328, B:N.328, A:Q.257 Water bridges: B:T.75, B:R.314, B:R.314, B:H.315, B:A.331, A:R.249, A:D.253, A:D.253, A:D.253, A:Q.257, A:K.260 Salt bridges: B:R.314, B:H.315, A:K.260

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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