Structure of Compound 4 bound to human ALDH1A1

  • Classification: OXIDOREDUCTASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2023-06-01 Released: 2024-05-01 
  • Deposition Author(s): Hurley, T.D.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Resolution: 1.86 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

Starting Model: experimental
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Development of substituted benzimidazoles as inhibitors of human aldehyde dehydrogenase 1A isoenzymes.

Takahashi, C.Chtcherbinine, M.Huddle, B.C.Wilson, M.W.Emmel, T.Hohlman, R.M.McGonigal, S.Buckanovich, R.J.Larsen, S.D.Hurley, T.D.

(2024) Chem Biol Interact 391: 110910-110910

  • DOI: https://doi.org/10.1016/j.cbi.2024.110910
  • Primary Citation of Related Structures:  
    8T0N, 8T0T

  • PubMed Abstract: 

    Aldehyde dehydrogenase 1A (ALDH1A) isoforms may be a useful target for overcoming chemotherapy resistance in high-grade serous ovarian cancer (HGSOC) and other solid tumor cancers. However, as different cancers express different ALDH1A isoforms, isoform selective inhibitors may have a limited therapeutic scope. Furthermore, resistance to an ALDH1A isoform selective inhibitor could arise via induction of expression of other ALDH1A isoforms. As such, we have focused on the development of pan-ALDH1A inhibitors, rather than on ALDH1A isoform selective compounds. Herein, we report the development of a new group of pan-ALDH1A inhibitors to assess whether broad spectrum ALDH1A inhibition is an effective adjunct to chemotherapy in HGSOC. Optimization of the CM10 scaffold, aided by ALDH1A1 crystal structures, led to improved biochemical potencies, improved cellular efficacy as demonstrated by reduction in ALDEFLUOR signal in HGSOC cells, and substantial improvements in liver microsomal stability. Based on this work we identified two compounds 17 and 25 suitable for future in vivo proof of concept experiments.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde dehydrogenase 1A1501Homo sapiensMutation(s): 1 
EC: (PDB Primary Data), (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P00352 (Homo sapiens)
Explore P00352 
Go to UniProtKB:  P00352
GTEx:  ENSG00000165092 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00352
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.86 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.267α = 90
b = 109.267β = 90
c = 83.168γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2024-05-01 
  • Deposition Author(s): Hurley, T.D.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA214567

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release