11CL | pdb_000011cl

Structure of human TRPV1 in complex with Asivatrep

PDB DOI: https://doi.org/10.2210/pdb11CL/pdb
EM Map EMD-75618: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2026-02-17 Released: 2026-06-03
Deposition Author(s): Lopez, K.E., Van Horn, W.D.
Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), American Heart Association

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

TRPV1 antagonism occurs through diverse structural mechanisms.

Lopez, K.E., Paduda, A.S., Derrick, M.J., Van Horn, W.D.

(2026) bioRxiv

PubMed: 42094379 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.64898/2026.04.27.721197
Primary Citation Related Structures:
11CJ, 11CK, 11CL, 11CN, 11CO

PubMed Abstract:
Transient receptor potential vanilloid 1 (TRPV1) ion channel mediates thermosensation and pain and is a target for non-addictive analgesics; however, clinical candidates have failed due to thermoregulatory side effects. Limited structural data for human TRPV1 (hTRPV1) bound to clinically relevant antagonists has constrained mechanistic insight. Using chemoinformatics-informed cryo-EM and BRET assays, we define the structural basis of antagonism across diverse chemotypes, including failed clinical compounds. A structure of hTRPV1 bound to 6-iodo-dihydrocapsaicin shows how a single substitution converts an agonist into an antagonist. Additional structures with Asivatrep, Mavatrep, and JNJ-17203212 reveal vanilloid pocket plasticity and divergent interaction networks, including lipid co-binding. Despite this diversity, antagonists converge on a conserved inhibited state, showing high potency is maintained across flexible binding modes. These findings redefine our understanding of hTRPV1 antagonism and illustrate how chemically diverse ligands stabilize an inhibited state in polymodal ion channels, laying groundwork for next-generation analgesics with improved safety.

Organizational Affiliation

School of Molecular Sciences, Arizona State University, 551 E. University Drive, Tempe, AZ 85287.

Macromolecule Content

Total Structure Weight: 500.22 kDa
Atom Count: 17,476
Modeled Residue Count: 2,124
Deposited Residue Count: 4,400
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 1	A, B [auth C], C [auth D], D [auth B]	1,100	Homo sapiens	Mutation(s): 1 Gene Names: TRPV1, VR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NER1 (Homo sapiens) Explore Q8NER1 Go to UniProtKB: Q8NER1
PHAROS: Q8NER1 GTEx: ENSG00000196689
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NER1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1C8J( Subject of Investigation/LOI) Query on A1C8J Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth C] SDF format, chain I [auth D] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain I [auth D] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain I [auth D] mmCIF format, chain K [auth B]	E [auth A], G [auth C], I [auth D], K [auth B]	(2E)-N-{(1R)-1-[3,5-difluoro-4-(methanesulfonamido)phenyl]ethyl}-3-[2-propyl-6-(trifluoromethyl)pyridin-3-yl]prop-2-enamide C₂₁ H₂₂ F₅ N₃ O₃ S UKGJZDSUJSPAJL-YPUOHESYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth C] Focus chain I [auth D] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth C] Focus chain I [auth D] Focus chain K [auth B]
LFA Query on LFA Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain J [auth D] SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain H [auth C] MOL2 format, chain J [auth D] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain H [auth C] mmCIF format, chain J [auth D] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth C], J [auth D], L [auth B]	EICOSANE C₂₀ H₄₂ CBFCDTFDPHXCNY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth C] Focus chain J [auth D] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth C] Focus chain J [auth D] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.21.2
MODEL REFINEMENT	Coot	0.9.8.93

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-03

Deposition Author(s):

Lopez, K.E.

Van Horn, W.D.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS119505
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM141933
American Heart Association	United States	23POST1029540