9R6N | pdb_00009r6n

Crystal structure of ALDH1A2 in complex with KyA33


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.177 (Depositor), 0.177 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Targeting autocrine retinoic acid signaling by ALDH1A2 inhibition enhances antitumor dendritic cell vaccine efficacy.

Fang, C.Esposito, M.Hars, U.Byrne, R.T.Song, B.Huang, J.Roichman, A.Shue, L.Cheng, X.Proudfoot, J.Zhao, D.Wei, Y.Cristea, I.M.Rabinowitz, J.D.Kang, Y.

(2026) Nat Immunol 

  • DOI: https://doi.org/10.1038/s41590-025-02376-4
  • Primary Citation of Related Structures:  
    9R6N

  • PubMed Abstract: 

    Strategies to stimulate dendritic cell (DC) activity, such as ex vivo generation and priming of DC vaccines, have been explored as cancer immunotherapies owing to their potential to elicit antitumor T cell responses. Despite decades of research, the success of DC vaccines has been limited, potentially because of unidentified tolerance-enforcing mechanisms. Here we show that GM-CSF-IL-4-induced differentiating DCs express ALDH1A2 and produce retinoic acid, inhibiting DC maturation. Genetic knockout of Aldh1a2 releases this natural brake and enhances DC function. We further develop an ALDH1A2 inhibitor with high potency, favorable drug-like properties and no evidence of off-target effects. Treatment with this inhibitor promotes DC activity, which in turn enhances antigen-specific T cell responses, improving the efficacy of DC vaccines. Our study demonstrates the unique role of the ALDH1A2-retinoic acid axis in regulating DC functions and further presents a new small-molecule inhibitor of ALDH1A2 as a potential immunotherapeutic agent for cancer.


  • Organizational Affiliation
    • Department of Molecular Biology, Princeton University, Princeton, NJ, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinal dehydrogenase 2
A, B, C, D
495Homo sapiensMutation(s): 0 
Gene Names: ALDH1A2RALDH2
EC: 1.2.1.36
UniProt & NIH Common Fund Data Resources
Find proteins for O94788 (Homo sapiens)
Explore O94788 
Go to UniProtKB:  O94788
PHAROS:  O94788
GTEx:  ENSG00000128918 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94788
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IDQ (Subject of Investigation/LOI)
Query on A1IDQ

Download Ideal Coordinates CCD File 
DA [auth C],
O [auth A],
OA [auth D],
W [auth B]
3-ethyl-~{N}-(8-methyl-2-oxidanylidene-3,4-dihydro-1~{H}-quinolin-6-yl)pyridine-4-carboxamide
C18 H19 N3 O2
CGDUSNFIWSMXHG-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
E [auth A]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
E [auth A],
EA [auth C],
F [auth A],
FA [auth D],
G [auth A],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
N [auth A],
NA [auth D],
P [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
X [auth C],
Y [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.177 (Depositor), 0.177 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.639α = 90
b = 140.045β = 93.93
c = 84.775γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
SCALAdata scaling
REFMACphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Database references