Crystal structure of human Aldehyde dehydrogenase 1A3 in complex with MF13 inhibitor compound

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 

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Progress in the Field of Aldehyde Dehydrogenase Inhibitors: Novel Imidazo[1,2- a ]pyridines against the 1A Family.

Quattrini, L.Gelardi, E.L.M.Petrarolo, G.Colombo, G.Ferraris, D.M.Picarazzi, F.Rizzi, M.Garavaglia, S.La Motta, C.

(2020) ACS Med Chem Lett 11: 963-970

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00686
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Members of the aldehyde dehydrogenase 1A family are commonly acknowledged as hallmarks of cancer stem cells, and their overexpression is significantly associated with poor prognosis in different types of malignancies. Accordingly, treatments targeting these enzymes may represent a successful strategy to fight cancer. In this work we describe a novel series of imidazo[1,2- a ]pyridines, designed as aldehyde dehydrogenase inhibitors by means of a structure-based optimization of a previously developed lead. The novel compounds were evaluated in vitro for their activity and selectivity against the three isoforms of the ALDH1A family and investigated through crystallization and modeling studies for their ability to interact with the catalytic site of the 1A3 isoform. Compound 3f emerged as the first in class submicromolar competitive inhibitor of the target enzyme.

  • 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
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: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.296α = 90
b = 89.176β = 90
c = 159.236γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Italian Ministry of EducationItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references, Structure summary
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description