IDH1 R132H in complex with IDH125

Experimental Data Snapshot

  • Resolution: 2.34 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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

  • 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 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

    Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP] cytoplasmicA,
B [auth C],
C [auth B],
417Homo sapiensMutation(s): 1 
Gene Names: IDH1PICD
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
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NDP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth C],
K [auth B],
N [auth D]
C21 H30 N7 O17 P3
Query on 70P

Download Ideal Coordinates CCD File 
F [auth A],
I [auth C],
L [auth B],
O [auth D]
C18 H22 N4 O2
Query on FLC

Download Ideal Coordinates CCD File 
G [auth A],
J [auth C],
M [auth B],
P [auth D]
C6 H5 O7
Binding Affinity Annotations 
IDSourceBinding Affinity
70P BindingDB:  5SVF IC50: min: 296, max: 330.5 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • 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
XDSdata reduction
autoPROCdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Refinement description