SMTL ID : 5sun.1

IDH1 R132H in complex with IDH146

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 21 residues within 4Å: Chain A: K.75, A.77, T.78, I.79, T.80, R.85, N.99, L.291, G.292, E.309, H.312, G.313, T.314, V.315, T.316, R.317, H.318, T.330, N.331, D.378 Ligands: DMS.6 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.75, A:T.78, A:T.80, A:T.80, A:T.80, A:R.85, A:R.85, A:N.99, A:E.309, A:H.312, A:G.313, A:T.314, A:V.315, A:N.331 Water bridges: A:A.334 Salt bridges: A:R.317, A:H.318 pi-Stacking: A:H.312 NDP.7: 21 residues within 4Å: Chain A: K.263 Chain B: K.75, A.77, T.78, I.79, T.80, R.85, N.99, L.291, G.292, E.309, H.312, G.313, T.314, V.315, T.316, R.317, H.318, T.330, N.331, D.378 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.75, B:T.78, B:T.78, B:T.80, B:T.80, B:R.85, B:R.85, B:N.99, B:E.309, B:G.313, B:T.314, B:V.315, B:T.316, B:N.331, B:N.331 Water bridges: B:A.334 Salt bridges: B:R.317, B:H.318, A:K.263 pi-Stacking: B:H.312

2 x 70Q: 3-benzyl-N-[3-(dimethylsulfamoyl)phenyl]-4-oxo-3,4-dihydrophthalazine-1-carboxamide(Non-covalent)

70Q.2: 15 residues within 4Å: Chain A: R.112, E.113, A.114, I.116, W.127, K.129, P.130, I.131, I.133, A.261, M.262, E.265, G.266, W.270 Ligands: 70Q.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.114, A:W.127, A:I.131, A:I.131, A:I.133, A:I.133 pi-Stacking: A:W.127, A:W.127, A:W.127, A:W.270 70Q.8: 17 residues within 4Å: Chain B: R.112, E.113, A.114, I.116, W.127, K.129, I.131, I.133, V.258, A.261, M.262, S.264, E.265, G.266, W.270, M.294 Ligands: 70Q.2 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:R.112, B:A.114, B:W.127, B:I.131, B:I.131, B:I.131, B:I.133, B:V.258, B:V.258, B:W.270, B:W.270 pi-Stacking: B:W.127, B:W.127, B:W.127

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

SO4.3: 7 residues within 4Å: Chain A: H.173, N.174, F.175, E.176, E.177, G.178 Chain B: Q.188 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.174, A:E.176, A:E.177, A:E.177, B:Q.188 Salt bridges: A:H.173 SO4.4: 7 residues within 4Å: Chain A: Y.322, Q.326, E.327, T.328, N.396, T.397, F.398 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.328, A:T.397, A:F.398 SO4.9: 7 residues within 4Å: Chain A: Q.188 Chain B: H.173, N.174, F.175, E.176, E.177, G.178 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.176, B:E.177, B:G.178, A:Q.188 Salt bridges: B:H.173 SO4.10: 2 residues within 4Å: Chain B: K.154, E.156 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.154

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: R.317, H.318, M.321, E.327, K.377 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.317, A:H.318, A:S.329, A:K.377 Water bridges: A:Y.394 EDO.11: 3 residues within 4Å: Chain B: Y.322, G.325, Q.326 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.325

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 4 residues within 4Å: Chain A: T.80, S.97, N.99 Ligands: NDP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.97 DMS.12: 3 residues within 4Å: Chain B: T.80, S.97, N.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.97

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] cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isocitrate dehydrogenase [NADP] cytoplasmic

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