[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleNavigating from cellular phenotypic screen to clinical candidate: selective targeting of the NLRP3 inflammasome.
Journal, issue, pagesEMBO Mol Med, Vol. 17, Issue 1, Page 54-84, Year 2025
Publish dateDec 9, 2024
AuthorsRosalie Matico / Karolien Grauwen / Dhruv Chauhan / Xiaodi Yu / Irini Abdiaj / Suraj Adhikary / Ine Adriaensen / Garcia Molina Aranzazu / Jesus Alcázar / Michela Bassi / Ellen Brisse / Santiago Cañellas / Shubhra Chaudhuri / Francisca Delgado / Alejandro Diéguez-Vázquez / Marc Du Jardin / Victoria Eastham / Michael Finley / Tom Jacobs / Ken Keustermans / Robert Kuhn / Josep Llaveria / Jos Leenaerts / Maria Lourdes Linares / Maria Luz Martín / Rosa Martín-Pérez / Carlos Martínez / Robyn Miller / Frances M Muñoz / Michael E Muratore / Amber Nooyens / Laura Perez-Benito / Mathieu Perrier / Beth Pietrak / Jef Serré / Sujata Sharma / Marijke Somers / Javier Suarez / Gary Tresadern / Andres A Trabanco / Dries Van den Bulck / Michiel Van Gool / Filip Van Hauwermeiren / Teena Varghese / Juan Antonio Vega / Sameh A Youssef / Matthew J Edwards / Daniel Oehlrich / Nina Van Opdenbosch /
PubMed AbstractThe 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 ...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.
External linksEMBO Mol Med / PubMed:39653810 / PubMed Central
MethodsEM (single particle)
Resolution3.76 Å
Structure data

46855

9dh3

EMDB-46855, PDB-9dh3:
Cryo-EM structure of NLRP3 complex with Compound C
Method: EM (single particle) / Resolution: 3.76 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

PDB-1a4l:
ADA STRUCTURE COMPLEXED WITH DEOXYCOFORMYCIN AT PH 7.0

ChemComp-CPS:
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / detergent*YM

Source
  • homo sapiens (human)
KeywordsIMMUNE SYSTEM / NLRP3 Inflammasome / Small Molecule Inhibitors / and Drug Discovery

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more