SMTL ID : 5svn.1

Structure of IDH2 mutant R172K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 23 residues within 4Å: Chain A: K.73, A.75, T.76, I.77, T.78, R.83, N.97, L.288, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 Chain B: T.214, L.250, D.253, Q.257, K.260 24 PLIP interactions: 17 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:T.76, A:T.78, A:T.78, A:T.78, A:R.83, A:R.83, A:N.97, A:G.310, A:T.311, A:V.312, A:N.328, A:N.328, B:Q.257 Water bridges: A:K.73, A:E.306, A:R.314, A:A.331, B:R.249, B:D.253, B:D.253, B:D.253, B:K.260 Salt bridges: A:H.315, B:K.260 NDP.3: 23 residues within 4Å: Chain A: T.214, L.250, D.253, Q.257, K.260 Chain B: K.73, A.75, T.76, I.77, T.78, R.83, N.97, L.288, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 27 PLIP interactions: 9 interactions with chain A, 18 interactions with chain B Hydrogen bonds: A:D.253, A:Q.257, B:T.76, B:T.76, B:T.78, B:T.78, B:T.78, B:R.83, B:R.83, B:N.97, B:N.97, B:H.309, B:G.310, B:T.311, B:V.312, B:N.328 Water bridges: A:T.214, A:R.249, A:R.249, A:D.253, A:Q.257, A:K.260, B:R.101, B:R.314, B:A.331 Salt bridges: A:K.260, B:H.315

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 6 residues within 4Å: Chain A: P.206, Y.208, S.261, G.263, G.264, F.265 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.264 Water bridges: A:Q.257, A:Q.257 PEG.4: 5 residues within 4Å: Chain B: P.206, Y.208, S.261, G.263, F.265 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, X. et al., Allosteric Mutant IDH1 Inhibitors Reveal Mechanisms for IDH1 Mutant and Isoform Selectivity. Structure (2017)

Release Date

2017-02-08

Peptides

Isocitrate dehydrogenase [NADP], mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isocitrate dehydrogenase [NADP], mitochondrial