8RI2 | pdb_00008ri2

Crystal structure of NLRP3 in complex with inhibitor NP3-562


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.270 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.224 (Depositor) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8RI2

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of Potent, Orally Bioavailable, Tricyclic NLRP3 Inhibitors.

Velcicky, J.Janser, P.Gommermann, N.Brenneisen, S.Ilic, S.Vangrevelinghe, E.Stiefl, N.Boettcher, A.Arnold, C.Malinverni, C.Dawson, J.Murgasova, R.Desrayaud, S.Beltz, K.Hinniger, A.Dekker, C.Farady, C.J.Mackay, A.

(2024) J Med Chem 67: 1544-1562

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02098
  • Primary Citation Related Structures: 
    8RI2

  • PubMed Abstract: 

    NLRP3 is a molecular sensor recognizing a wide range of danger signals. Its activation leads to the assembly of an inflammasome that allows for activation of caspase-1 and subsequent maturation of IL-1β and IL-18, as well as cleavage of Gasdermin-d and pyroptotic cell death. The NLRP3 inflammasome has been implicated in a plethora of diseases including gout, type 2 diabetes, atherosclerosis, Alzheimer's disease, and cancer. In this publication, we describe the discovery of a novel, tricyclic, NLRP3-binding scaffold by high-throughput screening. The hit ( 1 ) could be optimized into an advanced compound NP3-562 demonstrating excellent potency in human whole blood and full inhibition of IL-1β release in a mouse acute peritonitis model at 30 mg/kg po dose. An X-ray structure of NP3-562 bound to the NLRP3 NACHT domain revealed a unique binding mode as compared to the known sulfonylurea-based inhibitors. In addition, NP3-562 shows also a good overall development profile.


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

Macromolecule Content 

  • Total Structure Weight: 65.02 kDa 
  • Atom Count: 4,004 
  • Modeled Residue Count: 486 
  • Deposited Residue Count: 550 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
A1H02
(Subject of Investigation/LOI)

Query on A1H02



Download:Ideal Coordinates CCD File
B [auth A]2-[4-chloranyl-9-oxidanylidene-12-(2-oxidanylpropan-2-yl)-5-thia-1,10,11-triazatricyclo[6.4.0.0^{2,6}]dodeca-2(6),3,7,11-tetraen-10-yl]-~{N}-[(3~{R})-1-methylpiperidin-3-yl]ethanamide
C19 H24 Cl N5 O3 S
AXAOJXUYQVCGBD-UHFFFAOYSA-N
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.270 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.224 (Depositor) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.238α = 90
b = 96.238β = 90
c = 267.973γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2024-01-17 
  • Deposition Author(s): Dekker, C.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Database references