9W4M | pdb_00009w4m

ratTRPV1 bound with antagonist AMG517

• PDB DOI: https://doi.org/10.2210/pdb9W4M/pdb
• EM Map EMD-65638: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12, Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-07-31 Released: 2025-11-26 
• Deposition Author(s): Gao, Y.H., Li, Z.X.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structures of TRPV1 bound by hyperthermia-inducing analgesics.

Gao, Y.H., Huang, Y.Z., Li, Z.X., Chen, X.Y., Shao, C.Y., Li, H.W., Liu, B., Yang, F., Chen, M.R., Lu, M.L., Zhu, M.X., Yang, F., Xiao, Y.B., Yu, Y.

(2026) Cell Rep 45: 116765-116765

• PubMed: 41447532 
• DOI: https://doi.org/10.1016/j.celrep.2025.116765
• Primary Citation Related Structures: 
  9W4M, 9W4N, 9W4T


• PubMed Abstract: 
  

  TRPV1, a member of the transient receptor potential vanilloid subfamily, mediates nociception and thermoregulation. TRPV1-targeting analgesics frequently induce hyperthermia, underscoring the need for structural insights to guide the development of safer compounds. Here, we determined the structures of rat TRPV1 bound to the clinical candidate analgesics AMG517, AMG9810, and SB366791. AMG517 and AMG9810 are deeply situated within the S3-S4 interface of the vanilloid pocket, where they interact with residues from the S3-S6 helices, as well as the S4-S5 linker. These interactions induce local deformations in the TRP-box and lower S6 helix, accompanied by a modest rotation of the S1-S4 bundle, leading to partial dilation of the lower gate. The distinct allosteric changes of AMG517 and AMG9810, compared with the non-hyperthermic ligand SB366791, suggest a structural basis by which TRPV1-targeting analgesics influence thermoregulation and provide insights for designing safer analogs.

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Organizational Affiliation: 
• Department of Basic Medicine, Schools of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.
Shenzhen Medical Academy of Research and Translation, Guangming District, Shenzhen, Guangdong, China.
Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
School of Life Science and Technology, China Pharmaceutical University, Nanjing, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.
Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
Department of Biophysics and Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. Electronic address: [e-mail].
Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China. Electronic address: [e-mail].
Department of Basic Medicine, Schools of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; School of Life Sciences and Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 563.63 kDa 
• Atom Count: 17,546 
• Modeled Residue Count: 2,148 
• Deposited Residue Count: 5,008 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily V member 1	A, B, C, D	1,252	Escherichia coli K-12, Rattus norvegicus This entity is chimeric	Mutation(s): 0  Gene Names: malE, b4034, JW3994, Trpv1, Vr1, Vr1l
UniProt
Find proteins for O35433 (Rattus norvegicus) Explore O35433  Go to UniProtKB:  O35433

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D6R	E [auth A], H [auth B], I [auth C], J [auth D]	~{N}-[4-[6-[4-(trifluoromethyl)phenyl]pyrimidin-4-yl]oxy-1,3-benzothiazol-2-yl]ethanamide C20 H13 F3 N4 O2 S YUTIXVXZQIQWGY-UHFFFAOYSA-N
NA	F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Gao, Y.H., Li, Z.X.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021ZD0203400

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release
  
• Version 1.1: 2026-05-06
  Changes: Data collection, Database references
• Version 1.2: 2026-05-13
  Changes: Data collection, Database references