9QC1 | pdb_00009qc1

Crystal structure of the neurotensin receptor 1 in complex with the small-molecule full agonist cp28a

• PDB DOI: https://doi.org/10.2210/pdb9QC1/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-03-04 Released: 2026-02-11 
• Deposition Author(s): Deluigi, M., Hilge, M., Plueckthun, A.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.12 Å
• R-Value Free: 
  0.322 (Depositor), 0.316 (DCC) 
• R-Value Work: 
  0.300 (Depositor), 0.301 (DCC) 

Starting Model: experimental

Literature

Docking of virtual libraries identifies small-molecule agonists of neurotensin receptors with analgesic activity.

Panel, N., Vo, D.D., Hubner, H., Deluigi, M., Pach, S., Belair, F., Weikert, D., Klenk, C., Hilge, M., Shiva, N., Brochu, I., Longpre, J.M., Ballgren, F., Saleh, A., Hu, H., Kapla, J., Kampen, S., Cabeza de Vaca, I., Kihlberg, J., Wettschureck, N., Sarret, P., Pluckthun, A., Gmeiner, P., Carlsson, J.

(2026) Nat Commun 17

• PubMed: 42486867 
• DOI: https://doi.org/10.1038/s41467-026-74990-1
• Primary Citation Related Structures: 
  9QC1, 9QD4


• PubMed Abstract: 
  

  Peptide-activated G protein-coupled receptors (GPCRs) play crucial roles in numerous diseases, but remain difficult therapeutic targets due to the challenges in developing small-molecule drugs. Here, we explore structure-based strategies to identify small-molecule agonists of neurotensin (NTS) receptors, which hold promise for developing non-opioid analgesics. Chemical libraries of drug-like molecules are first designed based on a receptor-peptide complex, and then 14.5 million compounds are computationally docked to the orthosteric binding site of the NTS ₁ receptor. A set of 39 top-ranked compounds is synthesized, and seven of these are experimentally confirmed to activate the NTS ₁ receptor. Structure-guided optimization yields NTS ₁ ligands with signaling signatures distinct from the endogenous peptide, and these compounds also exhibit high affinity for the NTS ₂ receptor. High-resolution crystal structures of two agonists bound to the NTS ₁ receptor confirm predicted binding modes and reveal key determinants of activation. In vivo, the compounds produce robust antinociception in rodents without inducing hypotension, consistent with a contribution of NTS ₂ receptor activity. To facilitate broader application of our virtual screening approach to peptide-binding GPCRs, we provide access to tailored chemical libraries containing billions of readily synthesizable compounds.

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Organizational Affiliation: 
• Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden. [e-mail].
Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden. [e-mail].
Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
Department of Biochemistry, University of Zurich, Zürich, Switzerland.
Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institute de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, Canada.
FAUNeW - Research Center New Bioactive Compounds, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen, Germany.
Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, Giessen, Germany.
Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
Department of Pharmacy, SciLifeLab Drug Discovery and Development, Uppsala University, Uppsala, Sweden.
Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden.
Centre for Molecular Medicine, Medical Faculty, Goethe University, Frankfurt am Main, Germany.
Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institute de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, Canada. [e-mail].
Department of Biochemistry, University of Zurich, Zürich, Switzerland. [e-mail].
Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany. [e-mail].
FAUNeW - Research Center New Bioactive Compounds, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen, Germany. [e-mail].
Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 55.96 kDa 
• Atom Count: 3,193 
• Modeled Residue Count: 455 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurotensin receptor type 1, DARPin fusion	A	500	Rattus norvegicus	Mutation(s): 26  Gene Names: Ntsr1, Ntsr
UniProt
Find proteins for P20789 (Rattus norvegicus) Explore P20789  Go to UniProtKB:  P20789

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1I5G	B [auth A], C [auth A]	(2~{S})-4-methyl-2-[[3-(5-methylthiophen-2-yl)-5-(5-thiophen-3-yl-1,2,3,4-tetrazol-1-yl)phenyl]carbonylamino]pentanoic acid C23 H23 N5 O3 S2 IXKSDMHVMIKEIX-IBGZPJMESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.12 Å
• R-Value Free:  0.322 (Depositor), 0.316 (DCC) 
• R-Value Work:  0.300 (Depositor), 0.301 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.661	α = 90
b = 215.887	β = 90
c = 95.623	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
Aimless	data scaling
Coot	model building
REFMAC	refinement
ISOLDE	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-11 
Deposition Author(s): Deluigi, M., Hilge, M., Plueckthun, A.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A_182334

Revision History  

• Version 1.0: 2026-02-11
  Type: Initial release
  
• Version 1.1: 2026-08-26
  Changes: Database references