9DH3

Cryo-EM structure of NLRP3 complex with Compound C


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

  • DOI: https://doi.org/10.1038/s44321-024-00181-4
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 3 chimera
A, B, C, D
1,267Homo sapiensMutation(s): 0 
Gene Names: malEb4034JW3994NLRP3C1orf7CIAS1NALP3PYPAF1
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ96P20P0AEX9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CPS
Query on CPS

Download Ideal Coordinates CCD File 
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
ADP
Query on ADP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
A1A4L (Subject of Investigation/LOI)
Query on A1A4L

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History & Funding Information