9GU4

Crystal structure of NLRP3 in complex with inhibitor NP3-253


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.264 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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Literature

Discovery of NP3-253, a Potent Brain Penetrant Inhibitor of the NLRP3 Inflammasome.

Mackay, A.Velcicky, J.Gommermann, N.Mattes, H.Janser, P.Wright, M.Dubois, C.Brenneisen, S.Ilic, S.Vangrevelinghe, E.Stiefl, N.Boettcher, A.Schoenboerner, M.Vogelsanger, M.Muller-Bentz, S.Kamke, M.Rubert, J.Kauffmann, M.Desrayaud, S.Trunzer, M.Srinivas, H.Hinniger, A.von Burg, N.Beltz, K.Dekker, C.Farady, C.J.

(2024) J Med Chem 67: 20780-20798

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02350
  • Primary Citation of Related Structures:  
    9GU4

  • PubMed Abstract: 

    Activation of the NLRP3 inflammasome in response to danger signals is a key innate immune mechanism and results in the production of the pro-inflammatory cytokines interleukin-1β (IL-1β) and interleukin-18 (IL-18) as well as pyroptotic cell death. Aberrant NLRP3 activation has been linked to many acute and chronic conditions ranging from atherosclerosis to Alzheimer's disease and cancer, and based on the clinical success of IL-1-targeting therapies, NLRP3 has emerged as an attractive therapeutic target. Herein we describe our discovery, characterization, and structure-based optimization of a pyridazine-based series of NLRP3 inhibitors initiating from an high-throughput screening campaign. The scaffold, exemplified by lead molecule NP3-253 , has excellent potency and physicochemical and pharmacokinetic properties, including good brain penetration. The establishment of pharmacokinetic/pharmacodynamic relationships in the periphery and central nervous system in mechanistic models facilitates the use of NP3-253 as a tool to further interrogate the biology of NLRP3 in peripheral and neuroinflammatory models.


  • 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
Expand
  • 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
A1IPJ (Subject of Investigation/LOI)
Query on A1IPJ

Download Ideal Coordinates CCD File 
B [auth A]2-[6-[[(3R)-1-ethylpiperidin-3-yl]amino]pyridazin-3-yl]-3-methyl-5-(trifluoromethyl)phenol
C19 H23 F3 N4 O
UVVZGYXCKGWWCC-CQSZACIVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.264 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.029α = 90
b = 97.029β = 90
c = 265.041γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
XDSdata reduction
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 A1IPJClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2024-12-11 
  • Deposition Author(s): Srinivas, H.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release
  • Version 1.1: 2024-12-25
    Changes: Database references