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- EMDB-64801: Structure-Guided Design of Picomolar-level Macrocyclic TRPC5 Chan... -

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Basic information

Entry
Database: EMDB / ID: EMD-64801
TitleStructure-Guided Design of Picomolar-level Macrocyclic TRPC5 Channel Inhibitors with Antidepressant Activity
Map data
Sample
  • Complex: Short transient receptor potential channel 5
    • Protein or peptide: Short transient receptor potential channel 5
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: (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
Keywordsion channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / negative regulation of dendrite morphogenesis / store-operated calcium channel activity / TRP channels / inositol 1,4,5 trisphosphate binding / cation channel complex / actinin binding / clathrin binding / regulation of cytosolic calcium ion concentration ...regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / negative regulation of dendrite morphogenesis / store-operated calcium channel activity / TRP channels / inositol 1,4,5 trisphosphate binding / cation channel complex / actinin binding / clathrin binding / regulation of cytosolic calcium ion concentration / positive regulation of axon extension / positive regulation of neuron differentiation / calcium channel complex / calcium ion transmembrane transport / calcium channel activity / neuron differentiation / presynapse / actin binding / growth cone / ATPase binding / positive regulation of cytosolic calcium ion concentration / neuron apoptotic process / neuronal cell body / positive regulation of cell population proliferation / dendrite / metal ion binding / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical 5 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeat / Ankyrin repeats (3 copies) / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...Transient receptor potential channel, canonical 5 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeat / Ankyrin repeats (3 copies) / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Short transient receptor potential channel 5
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsChe T / Zhang J / Xiong B / Cheng XY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Pharm Sin B / Year: 2026
Title: Structure-guided design of picomolar-level macrocyclic TRPC5 channel inhibitors with antidepressant activity.
Authors: Tong Che / Yixiang Chen / Xinyu Cheng / Han Hu / Xiaoyun Wu / Yuting Zhang / Xiaoqiang Yang / Yinzhen Liu / Hui Liu / Weiwei Nan / Shuangyan Wan / Mingxing Yang / Bo Zeng / Jian Li / Jin Zhang / Bing Xiong /
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 ...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 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.
History
DepositionMay 27, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64801.png

Downloads & links

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Map

FileDownload / File: emd_64801.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 400 pix.
= 384. Å		0.96 Å/pix.
x 400 pix.
= 384. Å		0.96 Å/pix.
x 400 pix.
= 384. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.1584669 - 2.0550814
Average (Standard dev.)0.005240248 (±0.06280299)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64801_half_map_1.map
Projections & Slices
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Slices (1/2)
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Half map: #1

Fileemd_64801_half_map_2.map
Projections & Slices
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Sample components

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Entire : Short transient receptor potential channel 5

EntireName: Short transient receptor potential channel 5
Components
  • Complex: Short transient receptor potential channel 5
    • Protein or peptide: Short transient receptor potential channel 5
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: (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

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Supramolecule #1: Short transient receptor potential channel 5

SupramoleculeName: Short transient receptor potential channel 5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Short transient receptor potential channel 5

MacromoleculeName: Short transient receptor potential channel 5 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 111.591078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAQLYYKKVN YSPYRDRIPL QIVRAETELS AEEKAFLSAV EKGDYATVKQ ALQEAEIYYN VNINCMDPLG RSALLIAIEN ENLEIMELL LNHSVYVGDA LLYAIRKEVV GAVELLLSYR KPSGEKQVPT LMMDTQFSEF TPDITPIMLA AHTNNYEIIK L LVQKRVTI ...String:
MAQLYYKKVN YSPYRDRIPL QIVRAETELS AEEKAFLSAV EKGDYATVKQ ALQEAEIYYN VNINCMDPLG RSALLIAIEN ENLEIMELL LNHSVYVGDA LLYAIRKEVV GAVELLLSYR KPSGEKQVPT LMMDTQFSEF TPDITPIMLA AHTNNYEIIK L LVQKRVTI PRPHQIRCNC VECVSSSEVD SLRHSRSRLN IYKALASPSL IALSSEDPIL TAFRLGWELK ELSKVENEFK AE YEELSQQ CKLFAKDLLD QARSSRELEI ILNHRDDHSE ELDPQKYHDL AKLKVAIKYH QKEFVAQPNC QQLLATLWYD GFP GWRRKH WVVKLLTCMT IGFLFPMLSI AYLISPRSNL GLFIKKPFIK FICHTASYLT FLFMLLLASQ HIVRTDLHVQ GPPP TVVEW MILPWVLGFI WGEIKEMWDG GFTEYIHDWW NLMDFAMNSL YLATISLKIV AYVKYNGSRP REEWEMWHPT LIAEA LFAI SNILSSLRLI SLFTANSHLG PLQISLGRML LDILKFLFIY CLVLLAFANG LNQLYFYYET RAIDEPNNCK GIRCEK QNN AFSTLFETLQ SLFWSVFGLL NLYVTNVKAR HEFTEFVGAT MFGTYNVISL VVLLNMLIAM MNNSYQLIAD HADIEWK FA RTKLWMSYFD EGGTLPPPFN IIPSPKSFLY LGNWFNNTFC PKRDPDGRRR RHNLRSFTER HADSLIQNQH YQEVIRNL V KRYVAAMIRN SKTNEGLTEE NFKELKQDIS SFRYEVLDLL GNRKHPRRSL STSSADFSQR DDTNDGSGGA RAKSKSVSF NVGCKKKACH GAPLIRTVPR ASGAQGKPKS ESSSKRSFMG PSFKKLGLFF SKFNGQTSEP TSEPMYTISD GIAQQHCMWQ DIRYSQMEK GKAEACSQSQ MNLGEVELGE IRGAAARSSE CPLACSSSLH CASGICSSNS KLLDSSEDVF ETWGEACDLL M HKWGDGQE EQVTTRL

UniProtKB: Short transient receptor potential channel 5

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: (E)-1-(4-chlorobenzyl)-3-fluoro-1-(3-hydroxypropyl)-1,1,1,1-tetra...

MacromoleculeName: (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
type: ligand / ID: 4 / Number of copies: 8 / Formula: A1EH7
Molecular weightTheoretical: 542.986 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.53 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 70237
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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