9L3F | pdb_00009l3f

Structure-Guided Design of Picomolar-level Macrocyclic TRPC5 Channel Inhibitors with Antidepressant Activity


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-guided design of picomolar-level macrocyclic TRPC5 channel inhibitors with antidepressant activity.

Che, T.Chen, Y.Cheng, X.Hu, H.Wu, X.Zhang, Y.Yang, X.Liu, Y.Liu, H.Nan, W.Wan, S.Yang, M.Zeng, B.Li, J.Zhang, J.Xiong, B.

(2026) Acta Pharm Sin B 16: 371-386

  • DOI: https://doi.org/10.1016/j.apsb.2025.10.028
  • Primary Citation of Related Structures:  
    9L3F, 9V6J

  • PubMed Abstract: 

    Recent advances in ion channel structural biology have enhanced structure-based drug design, yet lipid-occupied binding pockets-often large and flat-remain a major hurdle for developing selective small molecules. TRPC5, a brain-enriched channel regulating depression and anxiety, is a promising therapeutic target, but current preclinical candidates suffer from moderate off-target effects. To address this, we designed macrocyclic TRPC5 inhibitors using structure-guided macrocyclization, overcoming lipid-binding site challenges. Among these, JDIC-127 exhibited unprecedented potency with IC 50 of 374 pmol/L-200-fold more potent than HC-070-and exceptional selectivity. Its specificity arises from interactions with unique structural features near the S5 and S6 helices of TRPC5, minimizing activity against related TRPC channels and other ion channels. This selective inhibition aligns with preclinical evidence supporting JDIC-127's potential in treating neuropsychiatric disorders. The study demonstrates how macrocycles stabilize ligand conformations, enhance affinity, and achieve selectivity in lipid-dominated binding sites. It also highlights the synergy between macrocyclic design, cryo-EM, and computational modeling to address longstanding obstacles in ion channel drug discovery. JDIC-127 serves as a proof-of-concept for the application of macrocyclization in ion channel pharmacology, offering a roadmap for developing innovative therapeutics targeting TRP channels and beyond, with implications for a wide range of diseases.


  • Organizational Affiliation
    • The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Short transient receptor potential channel 5
A, B, C, D
765Mus musculusMutation(s): 0 
Gene Names: Trpc5Trp5Trrp5
UniProt
Find proteins for Q9QX29 (Mus musculus)
Explore Q9QX29 
Go to UniProtKB:  Q9QX29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QX29
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EH7 (Subject of Investigation/LOI)
Query on A1EH7

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
(E)-1-(4-chlorobenzyl)-3-fluoro-1-(3-hydroxypropyl)-1,1,1,1-tetrahydro-1H-2,4-dioxa-1(8,3)-purina-3(1,3)-benzenacyclodecaphane-1,1-dione
C27 H28 Cl F N4 O5
IKZSODIUDUBEIW-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32271260

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release
  • Version 1.1: 2026-02-18
    Changes: Data collection, Database references