SMTL ID : 5i96.1

Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with AG-221 (Enasidenib) Inhibitor.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: D.314, S.317 Chain B: D.291 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:S.317, B:D.291, H2O.1, H2O.9, H2O.13 CA.9: 3 residues within 4Å: Chain A: D.291 Chain B: D.314, D.318 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.314, B:D.318, A:D.291, H2O.29, H2O.32

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: K.280, K.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.280, A:K.282 GOL.3: 6 residues within 4Å: Chain A: D.271, K.272, H.273, Y.274, K.275, T.276 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:H.273, A:K.275, A:T.276, A:T.276 Water bridges: A:D.271, A:K.272, A:K.275, A:T.276, A:T.276, A:D.277 GOL.4: 7 residues within 4Å: Chain A: F.184, V.185, A.186, D.187, R.188 Chain B: F.196, W.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.187, A:D.187 GOL.5: 8 residues within 4Å: Chain A: G.409, A.410, M.411, N.428, E.429, H.430, F.431, L.432 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.409, A:M.411, A:M.411, A:N.428 GOL.10: 7 residues within 4Å: Chain A: F.196, W.207 Chain B: F.184, V.185, A.186, D.187, R.188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.185, B:D.187 Water bridges: B:R.188

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

NDP.6: 19 residues within 4Å: Chain A: K.112, A.114, 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 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:K.112, A:T.115, A:T.115, A:T.117, A:T.117, A:R.122, A:R.122, A:N.136, A:E.345, A:G.349, A:G.349, A:T.350, A:V.351, A:N.367, A:N.367 Water bridges: A:T.352, A:A.370, A:D.414 Salt bridges: A:R.353, A:H.354 NDP.12: 20 residues within 4Å: Chain B: K.112, A.114, 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 Ligands: ACT.14 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:K.112, B:T.115, B:T.117, B:T.117, B:T.117, B:R.122, B:R.122, B:N.136, B:E.345, B:G.349, B:G.349, B:T.350, B:V.351, B:N.367, B:N.367 Water bridges: B:E.345, B:E.345, B:A.370 Salt bridges: B:R.353, B:H.354

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

NA.7: 3 residues within 4Å: Chain A: N.136, E.343, E.345 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.343, A:E.345 NA.13: 3 residues within 4Å: Chain B: N.136, E.343, E.345 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.343

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

ACT.8: 2 residues within 4Å: Chain A: H.453, H.454 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.454 Salt bridges: A:H.454 ACT.14: 3 residues within 4Å: Chain B: T.117, S.134 Ligands: NDP.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.134 Water bridges: B:T.117, B:N.136

1 x 69Q: 2-methyl-1-[(4-[6-(trifluoromethyl)pyridin-2-yl]-6-{[2-(trifluoromethyl)pyridin-4-yl]amino}-1,3,5-triazin-2-yl)amino]propan-2-ol(Non-covalent)

69Q.11: 21 residues within 4Å: Chain A: W.164, V.297, W.306, Y.311, D.312, V.315, Q.316, I.319, L.320 Chain B: W.164, I.168, I.290, V.294, V.297, W.306, Y.311, D.312, V.315, Q.316, I.319, L.320 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:I.319, A:V.297, A:W.306, A:V.315, A:Q.316, A:I.319, A:L.320 Hydrogen bonds: B:Q.316, B:Q.316, A:Q.316 Halogen bonds: B:D.312

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yen, K. et al., AG-221, a First-in-Class Therapy Targeting Acute Myeloid Leukemia Harboring Oncogenic IDH2 Mutations. Cancer Discov (2017)

Release Date

2017-03-08

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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