7A6Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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:  
    7A6Q

  • 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.


Macromolecules
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
EC: 1.2.1.36
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

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

Download Ideal Coordinates CCD File 
D [auth A],
M [auth B]
3-(2-phenylimidazo[1,2-a]pyridin-6-yl)benzenecarbonitrile
C20 H13 N3
ZIPMVBBAKJZVIG-UHFFFAOYSA-N
R2K
Query on R2K

Download Ideal Coordinates CCD File 
O [auth B](3-oxidanylidene-3-sodiooxy-propanoyl)oxysodium
C3 H2 Na2 O4
PRWXGRGLHYDWPS-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
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]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
I [auth A],
Q [auth B],
R [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



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