SMTL ID : 6bl0.2 (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: 3 residues within 4Å: Chain A: D.275 Chain B: D.252 Ligands: ICT.2 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.275, B:D.252, H2O.1, H2O.2 MG.4: 3 residues within 4Å: Chain A: D.252 Chain B: D.275 Ligands: ICT.5 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.275, A:D.252, H2O.11, H2O.12

2 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.2: 14 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: MG.1, NAP.3 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:K.212, B:D.252, B:D.252, A:T.77, A:S.94, A:N.96 Salt bridges: B:K.212, A:R.100, A:R.100, A:R.109, A:R.132, A:R.132 Water bridges: A:R.100 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.4, NAP.6 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:K.212, A:D.252, B:S.94, B:N.96 Water bridges: A:T.214, B:T.77, B:T.77, B:R.100 Salt bridges: A:K.212, B:R.100, B:R.100, B:R.109, B:R.132, B:R.132

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

NAP.3: 24 residues within 4Å: Chain A: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, E.306, A.307, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, N.328, D.375 Chain B: L.250, D.253, K.260 Ligands: ICT.2 28 PLIP interactions: 24 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.75, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:A.308, A:H.309, A:G.310, A:G.310, A:T.311, A:V.312, A:N.328, B:D.253 Water bridges: A:T.75, A:E.306, A:T.313, A:T.313, A:T.313, A:H.315, A:H.315, A:A.331, B:D.253, B:D.253 Salt bridges: A:R.314, A:H.315, B:K.260 pi-Stacking: A:H.309 NAP.6: 24 residues within 4Å: Chain A: L.250, D.253, K.260 Chain B: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, E.306, A.307, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, N.328, D.375 Ligands: ICT.5 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.75, B:T.77, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:A.308, B:G.310, B:G.310, B:T.311, B:V.312, B:N.328, B:N.328, A:D.253 Water bridges: B:T.313, B:T.313, B:H.315, B:A.331 Salt bridges: B:R.314, B:H.315, A:K.260 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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