Crystal Structure of human ALDH1A3 in complex with 2,6-diphenylimidazo[1,2-a]pyridine (compound GA11) and NAD+

Experimental Data Snapshot

  • Resolution: 3.25 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.177 

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Imidazo[1,2-a]pyridine Derivatives as Aldehyde Dehydrogenase Inhibitors: Novel Chemotypes to Target Glioblastoma Stem Cells.

Quattrini, L.Gelardi, E.L.M.Coviello, V.Sartini, S.Ferraris, D.M.Mori, M.Nakano, I.Garavaglia, S.La Motta, C.

(2020) J Med Chem 63: 4603-4616

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01910
  • Primary Citation of Related Structures:  
    6S6W, 6TE5

  • PubMed Abstract: 

    Glioblastoma multiforme (GBM) is the deadliest form of brain tumor. It is known for its ability to escape the therapeutic options available to date thanks to the presence of a subset of cells endowed with stem-like properties and ability to resist to cytotoxic treatments. As the cytosolic enzyme aldehyde dehydrogenase 1A3 turns out to be overexpressed in these kinds of cells, playing a key role for their vitality, treatments targeting this enzyme may represent a successful strategy to fight GBM. In this work, we describe a novel class of imidazo[1,2- a ]pyridine derivatives as aldehyde dehydrogenase 1A3 inhibitors, reporting the evidence of their significance as novel drug candidates for the treatment of GBM. Besides showing an interesting functional profile, in terms of activity against the target enzyme and selectivity toward highly homologous isoenzymes, representative examples of the series also showed a nanomolar to picomolar efficacy against patient-derived GBM stem-like cells, thus proving the concept that targeting aldehyde dehydrogenase might represent a novel and promising way to combat GBM by striking its ability to divide immortally.

  • Organizational Affiliation

    Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde dehydrogenase family 1 member A3
A, B
489Homo 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: 3.25 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.177 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.557α = 90
b = 89.357β = 90
c = 159.037γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Italian Ministry of EducationItalyFAR_2016

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description