SMTL ID : 6io0.1

Human IDH1 R132C mutant complexed with compound A.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x AOU: (2E)-3-{3-[3-(2,6-dichlorophenyl)-5-(propan-2-yl)-1,2-oxazole-4-carbonyl]-1-methyl-1H-indol-7-yl}prop-2-enoic acid(Non-covalent)

AOU.1: 16 residues within 4Å: Chain A: A.111, R.119, L.120, V.121, W.124, I.128, I.130, V.255, M.259, W.267, C.269, S.278, V.281 Chain B: Q.277, S.280, V.281 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.120, A:V.121, A:W.124, A:W.124, A:I.130, A:W.267, B:V.281 Hydrogen bonds: A:I.128 Water bridges: A:L.120 Salt bridges: A:R.119 AOU.12: 16 residues within 4Å: Chain A: V.281, G.284 Chain B: A.111, R.119, L.120, V.121, W.124, I.128, I.130, V.255, M.259, W.267, S.278, V.281, A.282, M.291 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.111, B:L.120, B:L.120, B:V.121, B:W.124, B:W.124, B:I.130, B:W.267, B:W.267, B:V.281 Water bridges: B:A.111, B:P.118, B:L.120, B:I.128 Salt bridges: B:R.119

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

NDP.2: 20 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, H.309, G.310, T.311, V.312, T.313, H.315, T.327, N.328, D.375 Ligands: CIT.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:T.75, A:T.77, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:E.306, A:H.309, A:G.310, A:G.310, A:T.311, A:V.312, A:N.328 Water bridges: A:H.315, A:A.331 Salt bridges: A:H.315 pi-Stacking: A:H.309 NDP.13: 22 residues within 4Å: Chain B: K.72, A.74, T.75, I.76, T.77, R.82, N.96, Q.283, L.288, G.289, E.306, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 Ligands: CIT.14 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:K.72, B:T.75, B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:E.306, B:G.310, B:G.310, B:T.311, B:V.312, B:N.328, B:N.328 Water bridges: B:Q.283, B:E.306, B:E.306, B:T.313, B:H.315, B:A.331 Salt bridges: B:R.314, B:H.315

3 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 5 residues within 4Å: Chain A: T.77, S.94, N.96, R.100 Ligands: NDP.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.94, A:N.96 Water bridges: A:T.77 Salt bridges: A:R.100 CIT.4: 5 residues within 4Å: Chain A: L.168, V.169, H.170, N.171 Chain B: Y.183 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Y.183, B:Y.183, A:H.170, A:N.171 Hydrophobic interactions: A:L.168, A:H.170 Salt bridges: A:H.170 CIT.14: 5 residues within 4Å: Chain B: T.77, S.94, N.96, R.100 Ligands: NDP.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.77, B:S.94, B:N.96 Water bridges: B:T.77 Salt bridges: B:R.100

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: S.6, G.7, G.8, E.36, L.37, D.38 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.6, A:G.8 GOL.6: 4 residues within 4Å: Chain A: R.140, M.182, Y.183, N.184 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.183, A:N.184, A:N.184 Water bridges: A:Y.183, A:Y.183 GOL.7: 6 residues within 4Å: Chain B: S.6, G.7, G.8, E.36, L.37, D.38 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.6, B:G.8 GOL.8: 6 residues within 4Å: Chain B: E.110, A.111, I.112, I.113, P.127, I.364 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.111, B:I.113, B:I.113 Water bridges: B:A.111, B:K.203, B:R.338 GOL.9: 5 residues within 4Å: Chain A: Y.183 Chain B: L.168, V.169, H.170, N.171 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.170, B:N.171 Water bridges: B:N.171 GOL.10: 6 residues within 4Å: Chain B: Y.319, G.322, Q.323, E.324, T.325, F.395 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.322, B:T.325, B:T.325 GOL.11: 4 residues within 4Å: Chain B: S.9, D.38, H.40, H.67 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.9, B:H.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Machida, Y. et al., A Potent Blood-Brain Barrier-Permeable Mutant IDH1 Inhibitor Suppresses the Growth of Glioblastoma with IDH1 Mutation in a Patient-Derived Orthotopic Xenograft Model. Mol.Cancer Ther. (2020)

Release Date

2019-10-30

Peptides

Isocitrate dehydrogenase [NADP] cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isocitrate dehydrogenase [NADP] cytoplasmic