9DH3 | pdb_00009dh3

Cryo-EM structure of NLRP3 complex with Compound C

PDB DOI: https://doi.org/10.2210/pdb9DH3/pdb
EM Map EMD-46855: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda ascovirus 1a
Mutation(s): No

Deposited: 2024-09-03 Released: 2024-12-25
Deposition Author(s): Matico, R., Grauwen, K., Van Gool, M., Muratore, E.M., Yu, X., Abdiaj, I., Adhikary, S., Adriaensen, I., Aranzazu, G.M., Alcazar, J., Bassi, M., Brisse, E., Canellas, S., Chaudhuri, S., Chauhan, D., Delgado, F., Dieguez-Vazquez, A., Du Jardin, M., Eastham, V., Finley, M., Jacobs, T., Keustermans, K., Kuhn, R., Llaveria, J., Leenaerts, J., Linares, M.L., Martin, M.L., Martinez, C., Miller, R., Munoz, F.M., Nooyens, A., Perez, L.B., Perrier, M., Pietrak, B., Serre, J., Sharma, S., Somers, M., Suarez, J., Tresadern, G., Trabanco, A.A., Van den Bulck, D., Van Hauwermeiren, F., Varghese, T., Vega, J.A., Youssef, S.A., Edwards, M.J., Oehlrich, D., Van Opdenbosch, N.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.76 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Navigating from cellular phenotypic screen to clinical candidate: selective targeting of the NLRP3 inflammasome.

Matico, R., Grauwen, K., Chauhan, D., Yu, X., Abdiaj, I., Adhikary, S., Adriaensen, I., Aranzazu, G.M., Alcazar, J., Bassi, M., Brisse, E., Canellas, S., Chaudhuri, S., Delgado, F., Dieguez-Vazquez, A., Du Jardin, M., Eastham, V., Finley, M., Jacobs, T., Keustermans, K., Kuhn, R., Llaveria, J., Leenaerts, J., Linares, M.L., Martin, M.L., Martin-Perez, R., Martinez, C., Miller, R., Munoz, F.M., Muratore, M.E., Nooyens, A., Perez-Benito, L., Perrier, M., Pietrak, B., Serre, J., Sharma, S., Somers, M., Suarez, J., Tresadern, G., Trabanco, A.A., Van den Bulck, D., Van Gool, M., Van Hauwermeiren, F., Varghese, T., Vega, J.A., Youssef, S.A., Edwards, M.J., Oehlrich, D., Van Opdenbosch, N.

(2025) EMBO Mol Med 17: 54-84

PubMed: 39653810 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s44321-024-00181-4
Primary Citation Related Structures:
9DH3

PubMed Abstract:
The NLRP3 inflammasome plays a pivotal role in host defense and drives inflammation against microbial threats, crystals, and danger-associated molecular patterns (DAMPs). Dysregulation of NLRP3 activity is associated with various human diseases, making it an attractive therapeutic target. Patients with NLRP3 mutations suffer from Cryopyrin-Associated Periodic Syndrome (CAPS) emphasizing the clinical significance of modulating NLRP3. In this study, we present the identification of a novel chemical class exhibiting selective and potent inhibition of the NLRP3 inflammasome. Through a comprehensive structure-activity relationship (SAR) campaign, we optimized the lead molecule, compound A, for in vivo applications. Extensive in vitro and in vivo characterization of compound A confirmed the high selectivity and potency positioning compound A as a promising clinical candidate for diseases associated with aberrant NLRP3 activity. This research contributes to the ongoing efforts in developing targeted therapies for conditions involving NLRP3-mediated inflammation, opening avenues for further preclinical and clinical investigations.

Organizational Affiliation

Janssen Research & Development, LLC, Discovery Technologies and Molecular Pharmacology (DTMP), Spring House, PA, 19044, USA.

Macromolecule Content

Total Structure Weight: 576.94 kDa
Atom Count: 37,752
Modeled Residue Count: 4,724
Deposited Residue Count: 5,068
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 3 chimera	A, B, C, D	1,267	Homo sapiens	Mutation(s): 0 Gene Names: malE, b4034, JW3994, NLRP3, C1orf7, CIAS1, NALP3, PYPAF1 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9 Go to UniProtKB: P0AEX9
Find proteins for Q96P20 (Homo sapiens) Explore Q96P20 Go to UniProtKB: Q96P20
PHAROS: Q96P20
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q96P20 P0AEX9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CPS Query on CPS Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain P [auth D] SDF format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C]	G [auth A], J [auth B], M [auth C], P [auth D]	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE C₃₂ H₅₈ N₂ O₇ S UMCMPZBLKLEWAF-BCTGSCMUSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
A1A4L (Subject of Investigation/LOI) Query on A1A4L Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain O [auth D] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C]	F [auth A], I [auth B], L [auth C], O [auth D]	2-[(4S)-5-ethyl-8-oxothieno[2',3':4,5]pyrrolo[1,2-d][1,2,4]triazin-7(8H)-yl]-N-(pyrimidin-4-yl)acetamide C₁₆ H₁₄ N₆ O₂ S CWNJFZLUBUHIRK-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]