5SVF

IDH1 R132H in complex with IDH125


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Allosteric Mutant IDH1 Inhibitors Reveal Mechanisms for IDH1 Mutant and Isoform Selectivity.

Xie, X.Baird, D.Bowen, K.Capka, V.Chen, J.Chenail, G.Cho, Y.Dooley, J.Farsidjani, A.Fortin, P.Kohls, D.Kulathila, R.Lin, F.McKay, D.Rodrigues, L.Sage, D.Toure, B.B.van der Plas, S.Wright, K.Xu, M.Yin, H.Levell, J.Pagliarini, R.A.

(2017) Structure 25: 506-513

  • DOI: 10.1016/j.str.2016.12.017
  • Primary Citation of Related Structures:  
    5SUN, 5SVO, 5SVN, 5SVF

  • PubMed Abstract: 
  • Oncogenic IDH1 and IDH2 mutations contribute to cancer via production of R-2-hydroxyglutarate (2-HG). Here, we characterize two structurally distinct mutant- and isoform-selective IDH1 inhibitors that inhibit 2-HG production. Both bind to an allosteric p ...

    Oncogenic IDH1 and IDH2 mutations contribute to cancer via production of R-2-hydroxyglutarate (2-HG). Here, we characterize two structurally distinct mutant- and isoform-selective IDH1 inhibitors that inhibit 2-HG production. Both bind to an allosteric pocket on IDH1, yet shape it differently, highlighting the plasticity of this site. Oncogenic IDH1 R132H mutation destabilizes an IDH1 "regulatory segment," which otherwise restricts compound access to the allosteric pocket. Regulatory segment destabilization in wild-type IDH1 promotes inhibitor binding, suggesting that destabilization is critical for mutant selectivity. We also report crystal structures of oncogenic IDH2 mutant isoforms, highlighting the fact that the analogous segment of IDH2 is not similarly destabilized. This intrinsic stability of IDH2 may contribute to observed inhibitor IDH1 isoform selectivity. Moreover, discrete residues in the IDH1 allosteric pocket that differ from IDH2 may also guide IDH1 isoform selectivity. These data provide a deeper understanding of how IDH1 inhibitors achieve mutant and isoform selectivity.


    Organizational Affiliation

    Oncology, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA. Electronic address: raymond.pagliarini@novartis.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP] cytoplasmic ABCD417Homo sapiensMutation(s): 1 
Gene Names: IDH1PICD
EC: 1.1.1.42
Find proteins for O75874 (Homo sapiens)
Explore O75874 
Go to UniProtKB:  O75874
NIH Common Fund Data Resources
PHAROS:  O75874
Protein Feature View
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  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
70PIC50:  220   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.979α = 90
b = 154.993β = 90
c = 162.989γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
AutoPROCdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2016-08-05 
  • Released Date: 2017-02-08 
  • Deposition Author(s): Xie, X., Kulathila, R.

Revision History 

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Database references