8ZEM

Crystal Structure of NLRP3 NACHT domain in complex with NP3-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.305 
  • R-Value Observed: 0.307 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Deep-Learning-Driven Discovery of SN3-1, a Potent NLRP3 Inhibitor with Therapeutic Potential for Inflammatory Diseases.

Shi, C.Gao, T.Lyu, W.Qiang, B.Chen, Y.Chen, Q.Zhang, L.Liu, Z.

(2024) J Med Chem 67: 17833-17854

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01857
  • Primary Citation of Related Structures:  
    8ZEM

  • PubMed Abstract: 

    The NLRP3 inflammasome plays a central role in the pathogenesis of various intractable human diseases, making it an urgent target for therapeutic intervention. Here, we report the development of SN3-1, a novel orally potent NLRP3 inhibitor, designed through a lead compound strategy centered on deep-learning-based molecular generative models. Our strategy enables rapid fragment enumeration and takes into account the synthetic accessibility of the compounds, thereby significantly enhancing the optimization of lead compounds and facilitating the discovery of potent inhibitors. X-ray crystallography provided insights into the SN3-1 inhibitory mechanism. SN3-1 has shown a favorable safety profile in both acute and chronic toxicity assessments and exhibits robust pharmacokinetic properties. Furthermore, SN3-1 demonstrated significant therapeutic efficacy in various disease models characterized by NLRP3 activation. This study introduces a potent candidate for developing NLRP3 inhibitors and significantly expands the repertoire of tools available for the discovery of novel inhibitors.


  • Organizational Affiliation

    State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NACHT, LRR and PYD domains-containing protein 3551Homo 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
A1D79
Query on A1D79

Download Ideal Coordinates CCD File 
B [auth A]1-[5-[2,3-bis(chloranyl)phenyl]-2,3-dihydro-1~{H}-inden-4-yl]-3-[4-(2-oxidanylpropan-2-yl)thiophen-2-yl]sulfonyl-urea
C23 H22 Cl2 N2 O4 S2
SZXAJFHUVSPWPP-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.305 
  • R-Value Observed: 0.307 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.246α = 90
b = 97.246β = 90
c = 256.792γ = 120
Software Package:
Software NamePurpose
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Database references, Structure summary