9LQ3 | pdb_00009lq3

Crystal structure of Linafexor-FXR complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.293 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.267 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 
    0.270 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9LQ3

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

A first-in-class pulsatile FXR agonist for bile-acid-related liver diseases.

Zang, Y.Shi, J.Zhao, G.Tang, B.Liu, M.Yao, B.Wang, G.Pan, H.Yang, S.Deng, R.Zhao, Y.Zhang, Z.Guo, H.R.Sun, D.D.Wang, H.Gao, L.Yu, J.Diao, X.Li, Y.Li, J.Xu, H.E.

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10633-1
  • Primary Citation Related Structures: 
    9LQ3

  • PubMed Abstract: 

    Nuclear receptors are central regulators of metabolism 1 , yet therapeutic strategies that enforce continuous receptor activation frequently lead to reduced efficacy and unacceptable toxicity. Here we report a first-principles drug design strategy that aligns pharmacokinetics with physiological signalling cycles. We developed linafexor, a potent non-bile-acid agonist of the farnesoid X receptor (FXR) 2 ; it is engineered for rapid systemic clearance, which enables pulsatile receptor activation that mirrors endogenous bile acid dynamics 3-5 . Linafexor has robust efficacy across multiple preclinical models of metabolic dysfunction-associated steatohepatitis 6 , liver fibrosis 7 , primary biliary cholangitis and primary sclerosing cholangitis 8,9 . Transcriptomic analyses reveal that, unlike long-acting FXR agonists 10,11 , linafexor preserves cyclic FXR signalling, avoids receptor downregulation and prevents broad transcriptional dysregulation. Direct manipulation of delivery patterns demonstrates that sustained FXR activation-independent of compound identity-induces severe toxicity, establishing activation duration as a determinant of therapeutic index. In phase 1 clinical studies (ClinicalTrials.gov; NCT05082779), linafexor administered once daily produces transient FXR pathway engagement, marked by (1) induction of FGF19 12-14 , a key endocrine mediator of bile acid feedback regulation; and (2) suppression of C4 15 , an intermediate reflecting hepatic bile acid synthesis, with no treatment-related adverse events. Together, these findings identify pulsatile FXR activation as a mechanistically grounded and clinically translatable strategy, and establish linafexor as a first-in-class therapeutic for bile acid-related liver diseases.


  • Organizational Affiliation
    • State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 28.43 kDa 
  • Atom Count: 1,921 
  • Modeled Residue Count: 235 
  • Deposited Residue Count: 239 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bile acid receptor228Homo sapiensMutation(s): 0 
Gene Names: NR1H4BARFXRHRR1RIP14
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI1 (Homo sapiens)
Explore Q96RI1 
Go to UniProtKB:  Q96RI1
PHAROS:  Q96RI1
GTEx:  ENSG00000012504 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RI1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2B [auth C]11Homo sapiensMutation(s): 0 
Gene Names: NCOA2BHLHE75SRC2TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ELK
(Subject of Investigation/LOI)

Query on A1ELK



Download:Ideal Coordinates CCD File
C [auth A]Linafexor
C28 H25 Cl2 F N4 O4
CEEANZUSISGCJL-VQFNDLOPSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.293 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.267 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 0.270 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.478α = 90
b = 67.455β = 90
c = 58.304γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-08-06 
  • Deposition Author(s): Yao, B., Li, Y.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Derived calculations, Structure summary
  • Version 1.2: 2026-06-24
    Changes: Database references