Crystal structure of human Aldehyde dehydrogenase 1A3 in complex with a selective inhibitor

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

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A specific inhibitor of ALDH1A3 regulates retinoic acid biosynthesis in glioma stem cells.

Li, J.Garavaglia, S.Ye, Z.Moretti, A.Belyaeva, O.V.Beiser, A.Ibrahim, M.Wilk, A.McClellan, S.Klyuyeva, A.V.Goggans, K.R.Kedishvili, N.Y.Salter, E.A.Wierzbicki, A.Migaud, M.E.Mullett, S.J.Yates, N.A.Camacho, C.J.Rizzi, M.Sobol, R.W.

(2021) Commun Biol 4: 1420-1420

  • DOI: https://doi.org/10.1038/s42003-021-02949-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Elevated aldehyde dehydrogenase (ALDH) activity correlates with poor outcome for many solid tumors as ALDHs may regulate cell proliferation and chemoresistance of cancer stem cells (CSCs). Accordingly, potent, and selective inhibitors of key ALDH enzymes may represent a novel CSC-directed treatment paradigm for ALDH + cancer types. Of the many ALDH isoforms, we and others have implicated the elevated expression of ALDH1A3 in mesenchymal glioma stem cells (MES GSCs) as a target for the development of novel therapeutics. To this end, our structure of human ALDH1A3 combined with in silico modeling identifies a selective, active-site inhibitor of ALDH1A3. The lead compound, MCI-INI-3, is a selective competitive inhibitor of human ALDH1A3 and shows poor inhibitory effect on the structurally related isoform ALDH1A1. Mass spectrometry-based cellular thermal shift analysis reveals that ALDH1A3 is the primary binding protein for MCI-INI-3 in MES GSC lysates. The inhibitory effect of MCI-INI-3 on retinoic acid biosynthesis is comparable with that of ALDH1A3 knockout, suggesting that effective inhibition of ALDH1A3 is achieved with MCI-INI-3. Further development is warranted to characterize the role of ALDH1A3 and retinoic acid biosynthesis in glioma stem cell growth and differentiation.

  • Organizational Affiliation

    Department of Chemistry, University of South Alabama, 6040 USA South Drive, Mobile, AL, 36688, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde dehydrogenase family 1 member A3
A, B, C, D
512Homo sapiensMutation(s): 0 
Gene Names: ALDH1A3ALDH6
UniProt & NIH Common Fund Data Resources
Find proteins for P47895 (Homo sapiens)
Explore P47895 
Go to UniProtKB:  P47895
PHAROS:  P47895
GTEx:  ENSG00000184254 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47895
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.03α = 90
b = 158.475β = 90
c = 168.646γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description