9JH3 | pdb_00009jh3

CMF-019 with APLNR-Gi complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Multiscale biased chemical space remodeling for developing APLNR agonists with anti-HFpEF efficacy.

Sun, Q.Tian, X.Tan, L.Deng, Y.Liu, S.Xiong, Y.Feng, Y.Wang, Y.Zhang, L.Zhu, J.Xiao, H.Shao, Z.Guo, Y.Yan, W.Li, T.Ouyang, L.

(2025) Proc Natl Acad Sci U S A 122: e2423432122-e2423432122

  • DOI: https://doi.org/10.1073/pnas.2423432122
  • Primary Citation of Related Structures:  
    9JH3

  • PubMed Abstract: 

    Heart failure with preserved ejection fraction (HFpEF) represents a significant global health burden, yet effective pharmacotherapies remain elusive. The angiotensin-like 1 receptor, also known as the apelin receptor (APLNR), is a promising target for treating HFpEF due to its role in modulating cardiovascular function. Despite the cardioprotective effects of endogenous ligand, apelin, achieving G-protein-biased agonism for therapeutic benefit poses a significant challenge. In this study, we unravel the biased signal transduction pathway mediated by a reported partial G i -protein-biased APLNR agonist CMF-019 and developed a biased chemical space remodeling approach to identify exclusive G-protein-biased agonists targeting APLNR. These agonists exhibited enhanced Gi-protein-biased function and protective effects in both in vitro and in vivo. Our findings not only enhance comprehension of APLNR-biased agonism but also establish drug design strategies for modifying and reshaping biased chemical landscapes in other G-protein-coupled receptors (GPCRs).


  • Organizational Affiliation
    • Department of Cardiovascular Surgery, Cardiovascular Surgery Research Laboratory, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1353Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
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Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1340Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Apelin receptorC [auth R]380Homo sapiensMutation(s): 0 
Gene Names: APLNRAGTRL1APJ
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Find proteins for P35414 (Homo sapiens)
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PHAROS:  P35414
GTEx:  ENSG00000134817 
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UniProt GroupP35414
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ScFv16D [auth S]250Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2E [auth Y]61Homo sapiensMutation(s): 0 
Gene Names: GNG2
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Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1D5N (Subject of Investigation/LOI)
Query on A1D5N

Download Ideal Coordinates CCD File 
F [auth R](3~{S})-5-methyl-3-[[1-pentan-3-yl-2-(thiophen-2-ylmethyl)benzimidazol-5-yl]carbonylamino]hexanoic acid
C25 H33 N3 O3 S
VCQKKZXFASLXAH-SFHVURJKSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31972916

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-05-14
    Changes: Data collection, Database references
  • Version 1.3: 2025-06-25
    Changes: Data collection