9LJX image
Deposition Date 2025-01-15
Release Date 2025-10-15
Last Version Date 2025-11-05
Entry Detail
PDB ID:
9LJX
Keywords:
Title:
Crystal Structure of the Heterodimeric HIF-2 Complex with Agonist SD-26
Biological Source:
Source Organism:
Mus musculus (Taxon ID: 10090)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.80 Å
R-Value Free:
0.26
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 1 21 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Aryl hydrocarbon receptor nuclear translocator
Gene (Uniprot):Arnt
Chain IDs:A
Chain Length:384
Number of Molecules:1
Biological Source:Mus musculus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Endothelial PAS domain-containing protein 1
Gene (Uniprot):Epas1
Chain IDs:B
Chain Length:368
Number of Molecules:1
Biological Source:Mus musculus
Ligand Molecules
Primary Citation
Structure-Based Optimization of HIF-2 alpha Agonists That Synergistically Enhance Erythropoietin Production with PHD Inhibitors.
J.Med.Chem. 68 21346 21365 (2025)
PMID: 41047546 DOI: 10.1021/acs.jmedchem.5c01257

Abstact

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.

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Primary Citation of related structures