SMTL ID : 6bkz.1

Novel Modes of Inhibition of Wild-Type IDH1: Non-equivalent Allosteric Inhibition with Cmpd3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 21 residues within 4Å: Chain A: K.72, A.74, T.75, I.76, T.77, R.82, N.96, S.287, G.289, E.306, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 Chain B: K.260 26 PLIP interactions: 20 interactions with chain A, 6 interactions with chain B 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:G.310, A:G.310, A:T.311, A:V.312, A:N.328, A:N.328 Water bridges: A:H.315, A:A.331, A:D.375, B:K.260, B:K.260, B:K.260, B:K.260 Salt bridges: A:R.314, A:H.315, B:K.260, B:K.260 pi-Stacking: A:H.309 NAP.3: 21 residues within 4Å: Chain A: K.260 Chain B: K.72, A.74, T.75, I.76, T.77, R.82, N.96, S.287, G.289, E.306, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 25 PLIP interactions: 23 interactions with chain B, 2 interactions with chain A Hydrogen bonds: 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:E.306, B:G.310, B:G.310, B:T.311, B:V.312, B:T.313, B:N.328, B:N.328 Water bridges: B:T.313, B:T.313, B:H.315, B:A.331, A:K.260 Salt bridges: B:R.314, B:H.315, A:K.260 pi-Stacking: B:H.309

2 x DWM: (7R)-1-[(4-fluorophenyl)methyl]-N-{3-[(1R)-1-hydroxyethyl]phenyl}-7-methyl-5-(1H-pyrrole-2-carbonyl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridine-3-carboxamide(Non-covalent)

DWM.2: 20 residues within 4Å: Chain A: A.111, I.113, R.119, L.120, W.124, P.127, I.128, V.255, M.259, W.267, S.278, V.281, A.282, G.284, Y.285, L.288 Chain B: L.120, V.121, M.259, V.281 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.111, A:R.119, A:L.120, A:W.124, A:I.128, A:W.267, A:A.282, A:L.288, B:L.120, B:V.121, B:V.281 Hydrogen bonds: A:I.128, A:V.281, A:Y.285, B:L.120 Water bridges: A:K.126 pi-Stacking: A:Y.285 Halogen bonds: A:V.255 DWM.4: 24 residues within 4Å: Chain A: L.120, M.259, V.276, V.281 Chain B: A.111, I.113, P.118, R.119, L.120, W.124, P.127, I.128, I.130, V.255, A.258, M.259, W.267, D.279, V.281, A.282, G.284, Y.285, L.288, M.291 22 PLIP interactions: 18 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.111, B:I.113, B:R.119, B:R.119, B:L.120, B:W.124, B:I.130, B:W.267, B:V.281, A:L.120, A:L.120, A:V.276, A:V.281 Hydrogen bonds: B:L.120, B:I.128, B:V.281, B:G.284 Water bridges: B:K.126 pi-Stacking: B:W.124, B:W.124, B:Y.285 Halogen bonds: B:V.255

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
B

Isocitrate dehydrogenase [NADP] cytoplasmic

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