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:  

  • 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 alloster ...

    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 IDH1R132H 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isocitrate dehydrogenase [NADP] cytoplasmic
A, C, B, 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
70P
Query on 70P

Download SDF File 
Download CCD File 
A, B, C, D
(4S)-3-(2-{[(1S)-1-phenylethyl]amino}pyrimidin-4-yl)-4-(propan-2-yl)-1,3-oxazolidin-2-one
C18 H22 N4 O2
CUTPLPKYQGWUBC-DZGCQCFKSA-N
 Ligand Interaction
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
70PIC50: 220 nM BINDINGMOAD
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 = 90.00
b = 154.993β = 90.00
c = 162.989γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
AutoPROCdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references