5TQH

IDH1 R132H mutant in complex with IDH889

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Optimization of 3-Pyrimidin-4-yl-oxazolidin-2-ones as Allosteric and Mutant Specific Inhibitors of IDH1.

Levell, J.R., Caferro, T., Chenail, G., Dix, I., Dooley, J., Firestone, B., Fortin, P.D., Giraldes, J., Gould, T., Growney, J.D., Jones, M.D., Kulathila, R., Lin, F., Liu, G., Mueller, A., van der Plas, S., Slocum, K., Smith, T., Terranova, R., Toure, B.B., Tyagi, V., Wagner, T., Xie, X., Xu, M., Yang, F.S., Zhou, L.X., Pagliarini, R., Cho, Y.S.

(2017) ACS Med Chem Lett 8: 151-156

  • DOI: 10.1021/acsmedchemlett.6b00334

  • PubMed Abstract: 

    • High throughput screening and subsequent hit validation identified 4-isopropyl-3-(2-((1-phenylethyl)amino)pyrimidin-4-yl)oxazolidin-2-one as a potent inhibitor of IDH1R132H. Synthesis of the four separate stereoisomers identified the (S,S)-diastereom ...

    High throughput screening and subsequent hit validation identified 4-isopropyl-3-(2-((1-phenylethyl)amino)pyrimidin-4-yl)oxazolidin-2-one as a potent inhibitor of IDH1R132H. Synthesis of the four separate stereoisomers identified the (S,S)-diastereomer (IDH125, 1f) as the most potent isomer. This also showed reasonable cellular activity and excellent selectivity vs IDH1wt. Initial structure-activity relationship exploration identified the key tolerances and potential for optimization. X-ray crystallography identified a functionally relevant allosteric binding site amenable to inhibitors, which can penetrate the blood-brain barrier, and aided rational optimization. Potency improvement and modulation of the physicochemical properties identified (S,S)-oxazolidinone IDH889 (5x) with good exposure and 2-HG inhibitory activity in a mutant IDH1 xenograft mouse model.

    Organizational Affiliation: 

    Novartis Institutes for Biomedical Research , 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isocitrate dehydrogenase [NADP] cytoplasmic
A, B, C, D
417Homo sapiensMutation(s): 1 
Gene Names: IDH1 (PICD)
EC: 1.1.1.42
Find proteins for O75874 (Homo sapiens)
Go to Gene View: IDH1
Go to UniProtKB:  O75874
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC
Download SDF File 
Download CCD File 
A, B, C, D
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
NDP
Query on NDP
Download SDF File 
Download CCD File 
A, B, C, D
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
7J2
Query on 7J2
Download SDF File 
Download CCD File 
A, B, C, D
(4S)-3-[2-({(1S)-1-[5-(4-fluoro-3-methylphenyl)pyrimidin-2-yl]ethyl}amino)pyrimidin-4-yl]-4-(propan-2-yl)-1,3-oxazolidin-2-one
C23 H25 F N6 O2
JDCYIMQAIKEACU-HNAYVOBHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7J2IC50: 20 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 81.731α = 90.00
b = 155.745β = 90.00
c = 163.048γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2016-10-24 
  • Released Date: 2017-01-25 
  • Deposition Author(s): Xie, X., Kulathila, R.

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-03-01
    Type: Database references