9HG4 | pdb_00009hg4

NACHT domain of NLRP3 in complex with DFV890


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 
    0.264 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view detailsBest fitted A1IUGClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Discovery of DFV890, a Potent Sulfonimidamide-Containing NLRP3 Inflammasome Inhibitor.

Shen, D.M.Byth, K.F.Bertheloot, D.Braams, S.Bradley, S.Dean, D.Dekker, C.El-Kattan, A.F.Franchi, L.Glick, G.D.Ghosh, S.Hinniger, A.Katz, J.D.Kitanovic, A.Lu, X.Olhava, E.J.Opipari, A.W.Sanchez, B.Seidel, H.M.Stunden, J.Stutz, A.Telling, A.Venkatraman, S.Winkler, D.G.Roush, W.R.

(2025) J Med Chem 68: 5529-5550

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02759
  • Primary Citation of Related Structures:  
    9HG4

  • PubMed Abstract: 

    The discovery of DFV890 (( R )- 1 ), a potent and selective NLRP3 antagonist, is described. Replacement of the sulfonyl urea core from the first-generation NLRP3 antagonist CRID3 with a sulfonimidamide core afforded a novel and potent series of NLRP3 antagonists. The (R)- enantiomers of the sulfonimidamide series were found to be consistently more potent than structurally related sulfonyl ureas. Replacement of the furan unit of CRID3 with a 5-substituted thiazole unit led to DFV890 (( R )- 1 ), which potently inhibited IL-1β production in THP-1 cells and in primary human cells, blocked multiple downstream effectors of NLRP3 activation, and substantially improved PK properties and significantly lowered the predicted human dose compared to that for CRID3. DFV890 (( R )- 1 ) was also effective in an air pouch model of gout.


  • Organizational Affiliation

    IFM Therapeutics, Boston, Massachusetts 02116, United States.


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: NLRP3C1orf7CIAS1NALP3PYPAF1
EC: 3.6.4
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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
A1IUG (Subject of Investigation/LOI)
Query on A1IUG

Download Ideal Coordinates CCD File 
B [auth A]1-[azanyl-oxidanylidene-[2-(2-oxidanylpropan-2-yl)-1,3-thiazol-5-yl]-$l^{6}-sulfanylidene]-3-(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)urea
C19 H24 N4 O3 S2
LHVWNNYPUDZLSH-MUUNZHRXSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free:  0.264 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.238α = 90
b = 96.238β = 90
c = 262.701γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view detailsBest fitted A1IUGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2025-03-19 
  • Deposition Author(s): Dekker, C.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Database references