Crystal structure of human aldehyde dehydrogenase 1A3 in complex with selective NR6 inhibitor compound

Experimental Data Snapshot

  • Resolution: 2.95 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

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A Selective Competitive Inhibitor of Aldehyde Dehydrogenase 1A3 Hinders Cancer Cell Growth, Invasiveness and Stemness In Vitro.

Gelardi, E.L.M.Colombo, G.Picarazzi, F.Ferraris, D.M.Mangione, A.Petrarolo, G.Aronica, E.Rizzi, M.Mori, M.La Motta, C.Garavaglia, S.

(2021) Cancers (Basel) 13

  • DOI: https://doi.org/10.3390/cancers13020356
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Aldehyde dehydrogenase 1A3 (ALDH1A3) belongs to an enzymatic superfamily composed by 19 different isoforms, with a scavenger role, involved in the oxidation of a plethora of aldehydes to the respective carboxylic acids, through a NAD+-dependent reaction. Previous clinical studies highlighted the high expression of ALDH1A3 in cancer stem cells (CSCs) correlated to a higher risk of cancer relapses, chemoresistance and a poor clinical outcome. We report on the structural, biochemical, and cellular characterization of NR6, a new selective ALDH1A3 inhibitor derived from an already published ALDH non-selective inhibitor with cytotoxic activity on glioblastoma and colorectal cancer cells. Crystal structure, through X-Ray analysis, showed that NR6 binds a non-conserved tyrosine residue of ALDH1A3 which drives the selectivity towards this isoform, as supported by computational binding simulations. Moreover, NR6 shows anti-metastatic activity in wound healing and invasion assays and induces the downregulation of cancer stem cell markers. Overall, our work confirms the role of ALDH1A3 as an important target in glioblastoma and colorectal cells and propose NR6 as a promising molecule for future preclinical studies.

  • Organizational Affiliation

    Department of Pharmaceutical Sciences, University of Piemonte Orientale, A. Avogadro, 28100 Novara, 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
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A],
L [auth B]
C21 H27 N7 O14 P2
R2Q (Subject of Investigation/LOI)
Query on R2Q

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D [auth A],
M [auth B]
C20 H13 N3
Query on R2K

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O [auth B](3-oxidanylidene-3-sodiooxy-propanoyl)oxysodium
C3 H2 Na2 O4
Query on GOL

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F [auth A]
G [auth A]
H [auth A]
J [auth A]
K [auth A]
F [auth A],
G [auth A],
H [auth A],
J [auth A],
K [auth A],
N [auth B],
P [auth B]
C3 H8 O3
Query on NA

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E [auth A],
I [auth A],
Q [auth B],
R [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.95 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.162α = 90
b = 89.509β = 90
c = 158.646γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata 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: 2021-02-17
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description