9R6N | pdb_00009r6n

Crystal structure of ALDH1A2 in complex with KyA33

PDB DOI: https://doi.org/10.2210/pdb9R6N/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-13 Released: 2025-11-19
Deposition Author(s): Fang, C., Esposito, M., Huang, J., Kang, Y.
Funding Organization(s): Not funded

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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 27: 250-264

PubMed: 41491403 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41590-025-02376-4
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 220.54 kDa
Atom Count: 19,120
Modeled Residue Count: 1,973
Deposited Residue Count: 1,980
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinal dehydrogenase 2	A, B, C, D	495	Homo sapiens	Mutation(s): 0 Gene Names: ALDH1A2, RALDH2 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O94788
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IDQ (Subject of Investigation/LOI) Query on A1IDQ Download:Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain W [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain W [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain W [auth B]	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		Interactions Focus chain DA [auth C] Focus chain O [auth A] Focus chain OA [auth D] Focus chain W [auth B] Interactions & Density Focus chain DA [auth C] Focus chain O [auth A] Focus chain OA [auth D] Focus chain W [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain P [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	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		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]