8WSM

NLRP3 NACHT domain in complex with compound 32


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of Novel NLRP3 Inflammasome Inhibitors Composed of an Oxazole Scaffold Bearing an Acylsulfamide.

Ohba, Y.Adachi, K.Furukawa, T.Nishimaru, T.Sakurai, K.Masuo, R.Inami, T.Orita, T.Akai, S.Adachi, T.Usui, K.Hamada, Y.Mori, M.Kurimoto, T.Wakashima, T.Akiyama, Y.Miyazaki, S.Noji, S.

(2023) ACS Med Chem Lett 14: 1833-1838

  • DOI: https://doi.org/10.1021/acsmedchemlett.3c00433
  • Primary Citation of Related Structures:  
    8WSM

  • PubMed Abstract: 

    The NLRP3 inflammasome plays an important role in the defense mechanism of the innate immune system and has recently attracted much attention as a drug target for various inflammatory disorders. Among the strategies for generating the novel chemotype in current drug discovery, scaffold hopping and bioisosteric replacement are known to be attractive approaches. As the results of our medicinal chemistry campaign, which involved exploration of core motifs using a ring closing approach, a five-membered oxazole-based scaffold was identified, and subsequent implementation of bioisosteric replacement led to discovery of a novel chemical class of NLRP3 inflammasome inhibitor bearing the acylsulfamide group. Further optimization of aniline and sulfamide moieties to improve potency in human whole blood assay led to the identification of the orally bioactive compound 32 in the LPS challenge model. Furthermore, compound 32 attenuated kidney injury in adriamycin-induced glomerulonephritis in mice. These investigations indicated that the NLRP3 inhibitor could be a potential therapeutic agent for glomerulonephritis.


  • Organizational Affiliation

    Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki Osaka 569-1125, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NACHT, LRR and PYD domains-containing protein 3550Homo sapiensMutation(s): 0 
Gene Names: NLRP3
UniProt & NIH Common Fund Data Resources
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 GroupQ96P20
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XE3 (Subject of Investigation/LOI)
Query on XE3

Download Ideal Coordinates CCD File 
D [auth A]2-[[2-methyl-5-(trifluoromethyl)phenyl]amino]-~{N}-(1,4-oxazepan-4-ylsulfonyl)-1,3-oxazole-4-carboxamide
C17 H19 F3 N4 O5 S
AXBUEIBPZRUIGE-UHFFFAOYSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.997α = 90
b = 96.997β = 90
c = 266.057γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

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: 2023-11-22
    Type: Initial release
  • Version 1.1: 2024-01-03
    Changes: Database references