8WUY | pdb_00008wuy

Crystal Structure of TR3 LBD in complex with para-positioned 3,4,5-trisubstituted benzene derivatives


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.243 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.203 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structure-based design and synthesis of anti-fibrotic compounds derived from para-positioned 3,4,5-trisubstituted benzene.

Hong, W.Xiao, T.Lin, G.Liu, C.Li, H.Li, Y.Hu, H.Wu, S.Wang, S.Liang, Z.Lin, T.Liu, J.Chen, X.

(2024) Bioorg Chem 144: 107113-107113

  • DOI: https://doi.org/10.1016/j.bioorg.2024.107113
  • Primary Citation Related Structures: 
    8WUY

  • PubMed Abstract: 

    Liver fibrosis is an abnormal wound-healing response to liver injuries. It can lead to liver cirrhosis, and even liver cancer and liver failure. There is a lack of treatment for liver fibrosis and it is of great importance to develop anti-fibrotic drugs. A pivotal event in the process of developing liver fibrosis is the activation of hepatic stellate cells (HSCs), in which the nuclear receptor Nur77 plays a crucial role. This study aimed to develop novel anti-fibrotic agents with Nur77 as the drug target by modifying the structure of THPN, a Nur77-binding and anti-melanoma compound. Specifically, a series of para-positioned 3,4,5-trisubstituted benzene ring compounds with long-chain backbone were generated and tested for anti-fibrotic activity. Among these compounds, compound A8 was with the most potent and Nur77-dependent inhibitory activity against TGF-β1-induced activation of HSCs. In a crystal structure analysis, compound A8 bound Nur77 in a peg-in-hole mode as THPN did but adopted a different conformation that could interfere the Nur77 interaction with AKT, which was previous shown to be important for an anti-fibrotic activity. In a cell-based assay, compound A8 indeed impeded the interaction between Nur77 and AKT leading to the stabilization of Nur77 without the activation of AKT. In a mouse model, compound A8 effectively suppressed the activation of AKT signaling pathway and up-regulated the cellular level of Nur77 to attenuate the HSCs activation and ameliorate liver fibrosis with no significant toxic side effects. Collectively, this work demonstrated that Nur77-targeting compound A8 is a promising anti-fibrotic drug candidate.


  • Organizational Affiliation
    • State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Xiamen University, Xiamen, China; Cancer Research Center of Xiamen University, Xiamen, China; Xiamen Key Laboratory of Clinical Efficacy and Evidence Studies of Traditional Chinese Medicine, The First Affiliated Hospital of Xiamen University, Xiamen, China; The First Affiliated Hospital of Xiamen University, Xiamen, China.

Macromolecule Content 

  • Total Structure Weight: 55.38 kDa 
  • Atom Count: 3,717 
  • Modeled Residue Count: 457 
  • Deposited Residue Count: 496 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor subfamily 4immunitygroup A member 1
A, B
248Homo sapiensMutation(s): 0 
Gene Names: NR4A1
UniProt & NIH Common Fund Data Resources
Find proteins for P22736 (Homo sapiens)
Explore P22736 
Go to UniProtKB:  P22736
PHAROS:  P22736
GTEx:  ENSG00000123358 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22736
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on XBF



Download:Ideal Coordinates CCD File
C [auth A]~{N}-methyl-~{N}-octyl-3,4,5-tris(oxidanyl)benzamide
C16 H25 N O4
HUVVKGRTMBOPNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.243 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.203 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.844α = 90
b = 76.441β = 90
c = 129.417γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Database references