SMTL ID : 6bl2.1 (1 other biounit)

Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of His315 with Cmpd15

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.275, D.279 Chain B: D.252 Ligands: ICT.2 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.252, A:D.275, H2O.1, H2O.6 CA.3: 4 residues within 4Å: Chain A: D.252 Chain B: D.275, D.279 Ligands: ICT.5 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.252, B:D.275, H2O.10, H2O.16

2 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.2: 13 residues within 4Å: Chain A: T.77, S.94, N.96, R.100, R.109, R.132, Y.139, D.275, A.308 Chain B: K.212, I.215, D.252 Ligands: CA.1 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.94, A:N.96, A:Y.139, A:D.275, B:K.212 Water bridges: A:T.77, A:T.77, A:R.109 Salt bridges: A:R.100, A:R.100, A:R.109, A:R.132, A:R.132, B:K.212 ICT.5: 13 residues within 4Å: Chain A: K.212, I.215, D.252 Chain B: T.77, S.94, N.96, R.100, R.109, R.132, Y.139, D.275, A.308 Ligands: CA.3 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.77, B:S.94, B:N.96, B:D.275, A:K.212 Water bridges: B:R.109, B:A.308 Salt bridges: B:R.100, B:R.100, B:R.109, B:R.132, B:R.132, A:K.212, A:K.212

2 x DWS: 3-[(6aS,7S,9S,10aS)-9-cyano-7-methyl-8-oxo-2-(phenylamino)-6,6a,7,8,9,10-hexahydrobenzo[h]quinazolin-10a(5H)-yl]benzoic acid(Covalent)

DWS.4: 15 residues within 4Å: Chain A: G.289, H.309, V.312, R.314, H.315, M.318, T.325, S.326, T.327, N.328, K.374, D.375, A.378, L.383 Chain B: K.260 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.314, A:T.327, A:A.378, A:L.383 Hydrogen bonds: A:S.326, A:D.375, A:D.375 pi-Stacking: A:H.309, A:H.315 Salt bridges: B:K.260 DWS.6: 15 residues within 4Å: Chain A: K.260 Chain B: G.289, H.309, V.312, R.314, H.315, M.318, T.325, S.326, T.327, N.328, K.374, D.375, A.378, L.383 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain B Salt bridges: A:K.260 Hydrophobic interactions: B:R.314, B:T.327, B:K.374, B:A.378, B:L.383 Hydrogen bonds: B:S.326, B:D.375, B:D.375 Water bridges: B:K.374 pi-Stacking: B:H.309

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jakob, C.G. et al., Novel Modes of Inhibition of Wild-Type Isocitrate Dehydrogenase 1 (IDH1): Direct Covalent Modification of His315. J. Med. Chem. (2018)

Release Date

2018-07-25

Peptides

Isocitrate dehydrogenase [NADP] cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Isocitrate dehydrogenase [NADP] cytoplasmic

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