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

Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of His315 with Cmpd1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.275, D.279 Chain B: D.252 Ligands: ICT.2 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.275, A:D.279, B:D.252, H2O.2, H2O.5 CA.4: 4 residues within 4Å: Chain A: D.252 Chain B: D.275, D.279 Ligands: ICT.5 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.252, B:D.275, B:D.279, H2O.23, H2O.26

2 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.2: 13 residues within 4Å: Chain A: T.77, S.94, N.96, R.100, R.109, R.132, Y.139, D.275, A.308 Chain B: K.212, I.215, D.252 Ligands: CA.1 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.94, A:N.96, A:Y.139, B:K.212 Water bridges: A:T.77, A:R.109, A:D.279, A:D.279, A:A.308 Salt bridges: A:R.100, A:R.100, A:R.109, A:R.132, A:R.132, B:K.212 ICT.5: 13 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: CA.4 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.77, B:S.94, B:N.96, A:K.212 Water bridges: B:R.109, B:D.279, B:D.279, A:D.252 Salt bridges: B:R.100, B:R.100, B:R.109, B:R.132, B:R.132, A:K.212

2 x DWP: (6aS,7S,9R,10aS)-7,10a-dimethyl-8-oxo-2-(phenylamino)-5,6,6a,7,8,9,10,10a-octahydrobenzo[h]quinazoline-9-carbonitrile(Covalent)

DWP.3: 12 residues within 4Å: Chain A: G.289, H.309, V.312, R.314, H.315, M.318, T.325, S.326, T.327, N.328, K.374, D.375 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.312, A:T.327, A:N.328 Hydrogen bonds: A:S.326, A:K.374, A:D.375, A:D.375 pi-Stacking: A:H.309 DWP.6: 12 residues within 4Å: Chain B: G.289, H.309, V.312, R.314, H.315, M.318, T.325, S.326, T.327, N.328, K.374, D.375 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.312, B:T.327, B:N.328 Hydrogen bonds: B:S.326, B:K.374, B:D.375 pi-Stacking: B:H.309

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
C

B
C

Isocitrate dehydrogenase [NADP] cytoplasmic

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