SMTL ID : 6vfz.1

Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with NADPH and AG-881 (Vorasidenib) Inhibitor.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

1 x 9UO: 6-(6-chloropyridin-2-yl)-N2,N4-bis[(2R)-1,1,1-trifluoropropan-2-yl]-1,3,5-triazine-2,4-diamine(Non-covalent)

9UO.1: 20 residues within 4Å: Chain A: W.164, V.294, V.297, L.298, Y.311, D.312, V.315, Q.316, I.319, L.320 Chain B: W.164, V.294, V.297, L.298, Y.311, D.312, V.315, Q.316, I.319, L.320 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:W.164, B:V.297, B:L.320, A:Y.311, A:V.315, A:I.319, A:L.320 Hydrogen bonds: B:Q.316, B:Q.316, A:Q.316, A:Q.316 Halogen bonds: A:D.312

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

NDP.2: 20 residues within 4Å: Chain A: K.112, A.114, T.115, I.116, T.117, R.122, N.136, L.327, G.328, E.345, H.348, G.349, T.350, V.351, T.352, R.353, H.354, T.366, N.367, D.414 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:T.115, A:T.115, A:T.117, A:T.117, A:R.122, A:R.122, A:G.349, A:G.349, A:T.350, A:V.351, A:R.353, A:R.353, A:N.367, A:N.367 Water bridges: A:T.115, A:T.352, A:H.354, A:A.370 Salt bridges: A:H.354 NDP.5: 18 residues within 4Å: Chain B: K.112, T.115, I.116, T.117, R.122, N.136, L.327, E.345, H.348, G.349, T.350, V.351, T.352, R.353, H.354, T.366, N.367, D.414 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:K.112, B:T.115, B:T.115, B:T.117, B:T.117, B:T.117, B:R.122, B:R.122, B:G.349, B:G.349, B:T.350, B:V.351, B:R.353, B:N.367, B:N.367 Water bridges: B:E.345, B:E.345, B:A.370 Salt bridges: B:H.354

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: D.314, D.318 Chain B: D.291 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.314, A:D.318, B:D.291, H2O.5, H2O.11 CA.6: 3 residues within 4Å: Chain A: D.291 Chain B: D.314, D.318 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.291, B:D.314, B:D.314, H2O.21, H2O.21

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: R.149, I.170, G.313, S.317 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.313 Water bridges: A:R.149 NA.7: 4 residues within 4Å: Chain B: R.149, I.170, G.313, S.317 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.313 Water bridges: B:R.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Konteatis, Z. et al., Vorasidenib (AG-881): A First-in-Class, Brain-Penetrant Dual Inhibitor of Mutant IDH1 and 2 for Treatment of Glioma. Acs Med.Chem.Lett. (2020)

Release Date

2020-02-05

Peptides

Isocitrate dehydrogenase [NADP], mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isocitrate dehydrogenase [NADP], mitochondrial

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