9SFG | pdb_00009sfg

Crystal structure of NLRP3 in complex with inhibitor NP3-742


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.279 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of NP3-742: A Structurally Diverse NLRP3 Inhibitor Identified through an Unusual Phenol Replacement.

Velcicky, J.Langlois, J.B.Wright, M.Janser, P.Angst, D.Arnold, C.Beltz, K.Brenneisen, S.Dubois, C.Dawson, J.Fischer, C.Gommermann, N.Heizmann, A.Ilic, S.Machauer, R.Maschlej, M.Monnerat, S.Pflieger, D.Ristov, J.Rubert, J.Schwalm, G.Smith, D.R.Srinivas, H.Steiner, R.Stojanovic, A.Troxler, T.Unterreiner, A.Vangrevelinghe, E.von Burg, N.Wunderlich, J.Farady, C.J.Mackay, A.

(2025) J Med Chem 68: 23532-23553

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02412
  • Primary Citation of Related Structures:  
    9SFG

  • PubMed Abstract: 

    NLRP3 is a molecular sensor present in innate immune cells which recognizes a variety of danger signals such as MSU, ATP, or Aβ. Upon activation, it seeds a protein complex termed the inflammasome, which leads to secretion of the proinflammatory cytokines IL-1β and IL-18 and initiates pyroptotic cell death. NLRP3 inflammasome activation has been associated with a wide range of diseases including atherosclerosis, gout, and cancer. In this publication, we describe the replacement of the phenol moiety with indoles in the recently described pyridazine scaffold. This replacement required a shift of the hydrogen bond donor from the " ortho " to the " meta " position, relative to the pyridazine ring. Initial indole analog 7 demonstrated a robust in vivo IL-1β inhibition, but also a significant hERG inhibition. Decreasing lipophilicity led to the discovery of NP3-742 , demonstrating a favorable overall profile including diminished hERG inhibition and in vivo efficacy in a mouse peritonitis model.


  • Organizational Affiliation
    • Novartis BioMedical Research, CH-4002 Basel, Switzerland.

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
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
A1JNK (Subject of Investigation/LOI)
Query on A1JNK

Download Ideal Coordinates CCD File 
B [auth A]5-methyl-~{N}-[(3~{R})-1-methylpiperidin-3-yl]-6-(2-methyl-1~{H}-pyrrolo[2,3-b]pyridin-6-yl)pyridazin-3-amine
C19 H24 N6
HNZKLSSKFNXSQZ-OAHLLOKOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.279 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.15α = 90
b = 96.15β = 90
c = 260.655γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-10-22 
  • Deposition Author(s): Srinivas, H.

Funding OrganizationLocationGrant Number
Other privateSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Database references