9LOI | pdb_00009loi

Crystal Structure of the Heterodimeric HIF-2 Complex with Agonist SD-16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 
    0.275 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structure-Based Optimization of HIF-2 alpha Agonists That Synergistically Enhance Erythropoietin Production with PHD Inhibitors.

Guo, M.Xu, W.Bai, Z.Chen, K.Li, F.Jin, Z.Chen, X.Shang, Q.Zhang, M.Diao, X.Xu, D.Zhang, H.Mu, K.Wang, Y.Ly, T.Li, L.Zhu, Y.Song, C.Zhao, H.Wan, X.Zhang, Y.Zhuang, J.Wu, D.

(2025) J Med Chem 68: 21346-21365

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01257
  • Primary Citation of Related Structures:  
    9LJX, 9LJY, 9LOH, 9LOI

  • PubMed Abstract: 

    Hypoxia-inducible factor 2α (HIF-2α) is a crucial transcription factor regulating various physiological processes, including angiogenesis and erythropoiesis. The activity of HIF-2α is mainly controlled through oxygen-dependent protein hydroxylation, mediated by prolyl hydroxylase domain (PHD) enzymes, leading to subsequent HIF-2α ubiquitination and degradation. While several small-molecule PHD inhibitors have already been clinically applied in renal anemia treatment by indirectly activating the HIF-2α pathway, direct HIF-2α agonists remain largely unexplored. Here, we developed derivatives of HIF-2α agonist M1001, identifying SD-10 through molecular/cellular evaluations. By determining its cocrystal structure with the heterodimeric HIF-2 protein complex, we precisely characterized its molecular mechanism of action. Notably, SD-10 exhibited remarkable synergy with Daprodustat, an approved PHD inhibitor, in stimulating erythropoietin (EPO) secretion both in cellular models and animal studies. These findings not only provide insights into HIF-2α activation mechanism, but also offer a promising lead compound for developing innovative treatments for renal anemia.


  • Organizational Affiliation
    • State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aryl hydrocarbon receptor nuclear translocator384Mus musculusMutation(s): 0 
Gene Names: Arnt
UniProt & NIH Common Fund Data Resources
Find proteins for P53762 (Mus musculus)
Explore P53762 
Go to UniProtKB:  P53762
IMPC:  MGI:88071
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53762
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Endothelial PAS domain-containing protein 1368Mus musculusMutation(s): 0 
Gene Names: Epas1Hif2a
UniProt & NIH Common Fund Data Resources
Find proteins for P97481 (Mus musculus)
Explore P97481 
Go to UniProtKB:  P97481
IMPC:  MGI:109169
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97481
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EKA (Subject of Investigation/LOI)
Query on A1EKA

Download Ideal Coordinates CCD File 
C [auth B]6-chloranyl-1,1-bis(oxidanylidene)-~{N}-(2-pyrrolidin-1-ylphenyl)-1,2-benzothiazol-3-amine
C17 H16 Cl N3 O2 S
LREBZGRACAYBHK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free:  0.275 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.642α = 90
b = 99.609β = 107.08
c = 77.66γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

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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: 2025-10-15
    Type: Initial release
  • Version 1.1: 2025-10-22
    Changes: Database references
  • Version 1.2: 2025-11-05
    Changes: Database references