5TQH

IDH1 R132H mutant in complex with IDH889

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    5TQH

  • 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 IDH1 R132H . Synthesis of the four separate stereoisomers identified the ( S , S )-diastereomer ( IDH125 , 1f ) as the most potent isomer ...

    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 IDH1 R132H . 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 IDH1 wt . 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP] cytoplasmicA, B, C, D417Homo sapiensMutation(s): 1 
Gene Names: IDH1, PICD
EC: 1.1.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for O75874 (Homo sapiens)
Explore O75874 
Go to UniProtKB:  O75874
PHAROS:  O75874
GTEx:  ENSG00000138413 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75874
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP
Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]		NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N		 Ligand Interaction
7J2
Query on 7J2
Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
K [auth C],
N [auth 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
FLC
Query on FLC
Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
O [auth D]		CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
7J2 BindingDB:  5TQH IC50: min: 14, max: 20 (nM) from 2 assay(s)
Binding MOAD:  5TQH IC50: 20 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.731α = 90
b = 155.745β = 90
c = 163.048γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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  (Full details and data files)

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