4UMX

IDH1 R132H in complex with cpd 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Selective Inhibition of Mutant Isocitrate Dehydrogenase 1 (Idh1) Via Disruption of a Metal Binding Network by an Allosteric Small Molecule.

Deng, G.Shen, J.Yin, M.Mcmanus, J.Mathieu, M.Gee, P.He, T.Shi, C.Bedel, O.Mclean, L.R.Le-Strat, F.Zhang, Y.Marquette, J.Gao, Q.Zhang, B.Rak, A.Hoffmann, D.Rooney, E.Vassort, A.Englaro, W.Li, Y.Patel, V.Adrian, F.Gross, S.Wiederschain, D.Cheng, H.Licht, S.

(2015) J Biol Chem 290: 762

  • DOI: 10.1074/jbc.M114.608497
  • Primary Citation of Related Structures:  
    4UMX, 4UMY

  • PubMed Abstract: 
  • Cancer-associated point mutations in isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) confer a neomorphic enzymatic activity: the reduction of α-ketoglutarate to d-2-hydroxyglutaric acid, which is proposed to act as an oncogenic metabolite by inducing hy ...

    Cancer-associated point mutations in isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) confer a neomorphic enzymatic activity: the reduction of α-ketoglutarate to d-2-hydroxyglutaric acid, which is proposed to act as an oncogenic metabolite by inducing hypermethylation of histones and DNA. Although selective inhibitors of mutant IDH1 and IDH2 have been identified and are currently under investigation as potential cancer therapeutics, the mechanistic basis for their selectivity is not yet well understood. A high throughput screen for selective inhibitors of IDH1 bearing the oncogenic mutation R132H identified compound 1, a bis-imidazole phenol that inhibits d-2-hydroxyglutaric acid production in cells. We investigated the mode of inhibition of compound 1 and a previously published IDH1 mutant inhibitor with a different chemical scaffold. Steady-state kinetics and biophysical studies show that both of these compounds selectively inhibit mutant IDH1 by binding to an allosteric site and that inhibition is competitive with respect to Mg(2+). A crystal structure of compound 1 complexed with R132H IDH1 indicates that the inhibitor binds at the dimer interface and makes direct contact with a residue involved in binding of the catalytically essential divalent cation. These results show that targeting a divalent cation binding residue can enable selective inhibition of mutant IDH1 and suggest that differences in magnesium binding between wild-type and mutant enzymes may contribute to the inhibitors' selectivity for the mutant enzyme.


    Organizational Affiliation

    From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC AB425Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
VVS
Query on VVS

Download Ideal Coordinates CCD File 
A
2,6-bis(1H-imidazol-1-ylmethyl)-4-(2,4,4-trimethylpentan-2-yl)phenol
C22 H30 N4 O
PCIJWPBOCDNTJF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VVSIC50:  11   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.408α = 90
b = 81.408β = 90
c = 305.917γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2014-11-26
    Changes: Database references
  • Version 1.2: 2015-01-14
    Changes: Refinement description
  • Version 1.3: 2015-01-21
    Changes: Database references
  • Version 1.4: 2017-08-23
    Changes: Data collection, Structure summary