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 

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Ligand Structure Quality Assessment 


This is version 1.2 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: 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.


Macromolecules
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],
D
417Homo sapiensMutation(s): 1 
Gene Names: IDH1PICD
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth C],
K [auth B],
N [auth D]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
70P
Query on 70P

Download Ideal Coordinates CCD File 
F [auth A],
I [auth C],
L [auth B],
O [auth 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
FLC
Query on FLC

Download Ideal Coordinates CCD File 
G [auth A],
J [auth C],
M [auth B],
P [auth D]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
Binding Affinity Annotations 
IDSourceBinding Affinity
70P BindingDB:  5SVF IC50: min: 150, max: 970 (nM) from 6 assay(s)
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

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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