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 8JR9 | pdb_00008jr9

Small molecule agonist (PCO371) bound to human parathyroid hormone receptor type 1 (PTH1R)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8JR9

This is version 1.5 of the entry. See complete history. 

Literature

Conserved class B GPCR activation by a biased intracellular agonist.

Zhao, L.H., He, Q., Yuan, Q., Gu, Y., He, X., Shan, H., Li, J., Wang, K., Li, Y., Hu, W., Wu, K., Shen, J., Xu, H.E.

(2023) Nature 621: 635-641

  • DOI: https://doi.org/10.1038/s41586-023-06467-w
  • Primary Citation Related Structures: 
    8JR9

  • PubMed Abstract: 

    Class B G-protein-coupled receptors (GPCRs), including glucagon-like peptide 1 receptor (GLP1R) and parathyroid hormone 1 receptor (PTH1R), are important drug targets 1-5 . Injectable peptide drugs targeting these receptors have been developed, but orally available small-molecule drugs remain under development 6,7 . Here we report the high-resolution structure of human PTH1R in complex with the stimulatory G protein (G s ) and a small-molecule agonist, PCO371, which reveals an unexpected binding mode of PCO371 at the cytoplasmic interface of PTH1R with G s . The PCO371-binding site is totally different from all binding sites previously reported for small molecules or peptide ligands in GPCRs. The residues that make up the PCO371-binding pocket are conserved in class B GPCRs, and a single alteration in PTH2R and two residue alterations in GLP1R convert these receptors to respond to PCO371. Functional assays reveal that PCO371 is a G-protein-biased agonist that is defective in promoting PTH1R-mediated arrestin signalling. Together, these results uncover a distinct binding site for designing small-molecule agonists for PTH1R and possibly other members of the class B GPCRs and define a receptor conformation that is specific only for G-protein activation but not arrestin signalling. These insights should facilitate the design of distinct types of class B GPCR small-molecule agonist for various therapeutic indications.


  • Organizational Affiliation: 
    • State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. zhaolihuawendy@simm.ac.cn.

Macromolecule Content 

  • Total Structure Weight: 158.83 kDa 
  • Atom Count: 7,893 
  • Modeled Residue Count: 1,014 
  • Deposited Residue Count: 1,402 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha-1361Bos taurusMutation(s): 0 
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
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 GroupsP63096P63092
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-1352Rattus norvegicusMutation(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
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]71Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
Entity Groups
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UniProt GroupP59768
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody 35D [auth N]140Lama glamaMutation(s): 0 
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Parathyroid hormone/parathyroid hormone-related peptide receptorE [auth R]478Homo sapiensMutation(s): 0 
Gene Names: PTH1R, PTHR, PTHR1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q03431 (Homo sapiens)
Explore Q03431 
Go to UniProtKB:  Q03431
PHAROS:  Q03431
GTEx:  ENSG00000160801 
Entity Groups
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UniProt GroupQ03431
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Reference Sequence

Small Molecules

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

Query on KHF



Download:Ideal Coordinates CCD File
F [auth R]PCO-371
C29 H32 F3 N5 O6 S
LDZJFVOUPUFOHX-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
KHF BindingDB:  8JR9 EC50: min: 2400, max: 4100 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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: 2023-08-02
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references
  • Version 1.2: 2023-09-27
    Changes: Derived calculations, Structure summary
  • Version 1.3: 2023-10-04
    Changes: Database references
  • Version 1.4: 2024-11-06
    Changes: Data collection, Structure summary
  • Version 1.5: 2026-09-02
    Changes: Data collection, Source and taxonomy