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 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
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wwPDB Validation 3D Report Full Report

Validation slider image for 9LQ3

Ligand Structure Quality Assessment 


This is version 1.3 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 655: 758-768

  • 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: NR1H4, BAR, FXR, HRR1, RIP14
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
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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: NCOA2, BHLHE75, SRC2, TIF2
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
  • Version 1.3: 2026-07-29
    Changes: Database references