9LHT | pdb_00009lht

Cryo-EM structure of inhibitor E3 bound human urea transporter A2.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9LHT

This is version 1.1 of the entry. See complete history

Literature

Structural characterization of the urea transporter bound to the orally bioavailable inhibitor E3.

Huang, S.M.Cai, B.Y.Liu, L.Yang, L.J.Li, Z.Zhang, C.Xiong, M.Y.Zhang, H.Li, Y.R.Huang, Z.Z.Sun, Y.Yang, B.X.Sun, J.P.

(2025) Acta Pharmacol Sin 46: 2989-2997

  • DOI: https://doi.org/10.1038/s41401-025-01595-7
  • Primary Citation Related Structures: 
    9LHT

  • PubMed Abstract: 

    Orally bioavailable inhibitors targeting the kidney urea transporter (UT) have the potential to serve as salt-sparing diuretics by employing a urea-selective diuretic mechanism of action distinct from that of diuretics targeting salt transporters. To elucidate the mechanism by which oral inhibitors interact with UTs, we solved the structure of a newly developed inhibitor, E3, with UT-A2 using cryo-electron microscopy. Through structural analysis and binding free energy calculations, we not only revealed the binding mode of E3 to UT-A2 but also clarified the structural basis by which E3 serves as a common competitive inhibitor of human, mouse and rat UT-A/UT-B. E3 exerts its inhibitory effect by competitively binding to the conserved Q-T-T-Q motif in the urea binding pockets of the transport channel. Moreover, we discovered that the BSBP region of UT can serve as a key region for enhancing the inhibitory potency of E3 with different UTs, which provides valuable structural insights for designing and modifying high-affinity UT inhibitors that act as diuretics.


  • Organizational Affiliation
    • Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, 100191, China. huangshenming@jnu.edu.cn.

Macromolecule Content 

  • Total Structure Weight: 132.57 kDa 
  • Atom Count: 7,674 
  • Modeled Residue Count: 984 
  • Deposited Residue Count: 1,191 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Urea transporter 2
A, B, C
397Homo sapiensMutation(s): 0 
Gene Names: SLC14A2HUT2UT2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15849 (Homo sapiens)
Explore Q15849 
Go to UniProtKB:  Q15849
PHAROS:  Q15849
GTEx:  ENSG00000132874 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15849
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82304601

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Data collection, Database references