9J5W | pdb_00009j5w

Cryo-EM Structure of URAT1 in Complex with Benzbromarone


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Inhibition of Urate Reabsorption in URAT1.

Fan, J.Xie, W.Ke, H.Zhang, J.Wang, J.Wang, H.Guo, N.Bai, Y.Lei, X.

(2025) JACS Au 5: 1308-1319

  • DOI: https://doi.org/10.1021/jacsau.4c01188
  • Primary Citation of Related Structures:  
    9J5W, 9J5X, 9J5Z

  • PubMed Abstract: 

    The urate transporter 1 (URAT1) is the primary urate transporter in the kidney responsible for urate reabsorption and, therefore, is crucial for urate homeostasis. Hyperuricemia causes the common human disease gout and other pathological consequences. Inhibition of urate reabsorption through URAT1 has been shown as a promising strategy in alleviating hyperuricemia, and clinical and preclinical drug candidates targeting URAT1 are emerging. However, how small molecules inhibit URAT1 remains undefined, and the lack of accurate URAT1 complex structures hinders the development of better therapeutics. Here, we present cryoelectron microscopy structures of a humanized rat URAT1 bound with benzbromarone, lingdolinurad, and verinurad, elucidating the structural basis for drug recognition and inhibition. The three small molecules reside in the URAT1 central cavity with different binding modes, locking URAT1 in an inward-facing conformation. This study provides mechanistic insights into the drug modulation of URAT1 and sheds light on the rational design of potential URAT1-specific therapeutics for treating hyperuricemia.


  • Organizational Affiliation
    • Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Organic Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Solute carrier family 22 member 12553Rattus norvegicusMutation(s): 0 
Gene Names: Slc22a12Urat1
Membrane Entity: Yes 
UniProt
Find proteins for Q3ZAV1 (Rattus norvegicus)
Explore Q3ZAV1 
Go to UniProtKB:  Q3ZAV1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3ZAV1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R75 (Subject of Investigation/LOI)
Query on R75

Download Ideal Coordinates CCD File 
B [auth A][3,5-bis(bromanyl)-4-oxidanyl-phenyl]-(2-ethyl-1-benzofuran-3-yl)methanone
C17 H12 Br2 O3
WHQCHUCQKNIQEC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-26
    Type: Initial release
  • Version 1.1: 2025-06-18
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-23
    Changes: Data collection