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

Validation slider image for 9JH3

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 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.

Macromolecule Content 

  • Total Structure Weight: 154.17 kDa 
  • Atom Count: 9,071 
  • Modeled Residue Count: 1,154 
  • Deposited Residue Count: 1,384 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
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)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63096
Sequence Annotations
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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)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
Entity Groups
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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
UniProt & NIH Common Fund Data Resources
Find proteins for P35414 (Homo sapiens)
Explore P35414 
Go to UniProtKB:  P35414
PHAROS:  P35414
GTEx:  ENSG00000134817 
Entity Groups
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UniProt GroupP35414
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ScFv16D [auth S]250Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
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
UniProt & NIH Common Fund Data Resources
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