9V6J | pdb_00009v6j

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

PDB DOI: https://doi.org/10.2210/pdb9V6J/pdb
EM Map EMD-64801: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-05-27 Released: 2025-12-03
Deposition Author(s): Che, T., Zhang, J., Xiong, B., Cheng, X.Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.23 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

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

Che, T., Zhang, J., Xiong, B., Cheng, X.Y.

To be published.

Macromolecule Content

Total Structure Weight: 897.92 kDa
Atom Count: 45,304
Modeled Residue Count: 5,504
Deposited Residue Count: 7,800
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short transient receptor potential channel 5	A, B, C, D, E A, B, C, D, E, F, G, H	975	Mus musculus	Mutation(s): 0 Gene Names: Trpc5, Trp5, Trrp5
UniProt
Find proteins for Q9QX29 (Mus musculus) Explore Q9QX29 Go to UniProtKB: Q9QX29
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9QX29
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EH7 (Subject of Investigation/LOI) Query on A1EH7 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain Z [auth F] SDF format, chain W [auth E] SDF format, chain T [auth D] SDF format, chain Q [auth C] SDF format, chain FA [auth H] SDF format, chain CA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Z [auth F] MOL2 format, chain W [auth E] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain FA [auth H] MOL2 format, chain CA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Z [auth F] mmCIF format, chain W [auth E] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain FA [auth H] mmCIF format, chain CA [auth G]	CA [auth G] FA [auth H] K [auth A] N [auth B] Q [auth C] CA [auth G], FA [auth H], K [auth A], N [auth B], Q [auth C], T [auth D], W [auth E], Z [auth F]	(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		Interactions Focus chain CA [auth G] Focus chain FA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain FA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain U [auth E] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain DA [auth H] SDF format, chain AA [auth G] MOL2 format, chain X [auth F] MOL2 format, chain U [auth E] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth H] MOL2 format, chain AA [auth G] mmCIF format, chain X [auth F] mmCIF format, chain U [auth E] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth H] mmCIF format, chain AA [auth G]	AA [auth G] DA [auth H] I [auth A] L [auth B] O [auth C] AA [auth G], DA [auth H], I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain V [auth E] SDF format, chain Y [auth F] SDF format, chain S [auth D] SDF format, chain EA [auth H] SDF format, chain BA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain S [auth D] MOL2 format, chain EA [auth H] MOL2 format, chain BA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth F] mmCIF format, chain S [auth D] mmCIF format, chain EA [auth H] mmCIF format, chain BA [auth G]	BA [auth G] EA [auth H] J [auth A] M [auth B] P [auth C] BA [auth G], EA [auth H], J [auth A], M [auth B], P [auth C], S [auth D], V [auth E], Y [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain EA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain EA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F]