SMTL ID : 6vei.1

Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with NADPH and AG-881 (Vorasidenib) Inhibitor

Coordinates

PDB Format

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: 18 residues within 4Å: Chain A: T.75, I.76, T.77, R.82, N.96, L.288, G.289, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:T.77, A:T.77, A:T.77, A:R.82, A:R.82, A:A.308, A:G.310, A:G.310, A:T.311, A:V.312, A:N.328, A:N.328 Water bridges: A:T.313, A:T.313, A:A.331 Salt bridges: A:R.314, A:H.315 pi-Stacking: A:H.309 NDP.8: 23 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, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 Ligands: PEG.10 27 PLIP interactions: 6 interactions with chain A, 21 interactions with chain B Hydrogen bonds: A:D.253, A:Q.257, A:Q.257, B:K.72, B:T.75, B:T.77, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:N.96, B:G.310, B:G.310, B:T.311, B:V.312, B:N.328, B:N.328 Water bridges: A:D.253, A:D.253, B:T.75, B:R.100, B:R.314, B:A.331 Salt bridges: A:K.260, B:H.315 pi-Stacking: B:H.309

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: Y.231, D.232, K.233, Q.234, Y.235, K.236, S.237 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.232, A:Q.234, A:Y.235, A:K.236, A:S.237 Water bridges: A:Q.238

1 x 33O: 3,6,9,12,15,18,21,24,27,30,33,36-dodecaoxaoctatriacontane-1,38-diol(Non-covalent)

33O.3: 7 residues within 4Å: Chain A: R.20, I.21, E.24, L.25, E.28, E.47, Q.320 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.20

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

PEG.4: 6 residues within 4Å: Chain A: M.199, S.202, V.296, G.300, H.342, K.345 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.202 Water bridges: A:Q.198, A:Q.198, A:R.338 PEG.5: 6 residues within 4Å: Chain A: P.206, Y.208, S.261, G.263, G.264, F.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.208, A:G.263 PEG.10: 9 residues within 4Å: Chain A: K.212, I.215, D.252 Chain B: T.77, S.94, N.96, Y.139, D.275 Ligands: NDP.8 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.77, B:S.94, B:Y.139, A:D.252 Water bridges: B:T.77, B:R.100, B:R.109, A:K.212, A:T.214 PEG.11: 6 residues within 4Å: Chain B: S.195, Q.198, M.199, S.202, V.296, P.298 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.202, B:S.202, B:P.298

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 3 residues within 4Å: Chain A: R.222, D.225, E.229 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.229 Water bridges: A:R.222, A:R.222, A:R.222 Salt bridges: A:R.222

1 x MLA: MALONIC ACID(Non-covalent)

MLA.7: 5 residues within 4Å: Chain A: L.168, V.169, H.170 Chain B: R.140, Y.183 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:L.168 Water bridges: A:H.170, A:N.171, B:T.142, B:T.142 Salt bridges: A:H.170, B:R.140

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.9: 19 residues within 4Å: Chain A: W.124, V.255, M.259, Y.272, D.273, V.276, Q.277, S.280, V.281 Chain B: W.124, V.255, A.258, M.259, W.267, D.273, V.276, Q.277, S.280, V.281 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.255, A:D.273, A:V.276, A:V.281 Hydrogen bonds: A:Q.277, A:S.280, B:Q.277, B:Q.277, B:S.280 Halogen bonds: B:D.273

1 x MLT: D-MALATE(Non-covalent)

MLT.12: 6 residues within 4Å: Chain A: R.140, T.142, Y.183 Chain B: L.168, V.169, H.170 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Water bridges: B:L.168, B:H.170, B:N.171 Salt bridges: B:H.170 Hydrogen bonds: A:Y.183

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] cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isocitrate dehydrogenase [NADP] cytoplasmic

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