9DKC | pdb_00009dkc

Structure of URAT1 in complex with TD-3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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Literature

Molecular basis of the urate transporter URAT1 inhibition by gout drugs.

Suo, Y.Fedor, J.G.Zhang, H.Tsolova, K.Shi, X.Sharma, K.Kumari, S.Borgnia, M.Zhan, P.Im, W.Lee, S.Y.

(2025) Nat Commun 16: 5178-5178

  • DOI: https://doi.org/10.1038/s41467-025-60480-3
  • Primary Citation of Related Structures:  
    9DK9, 9DKA, 9DKB, 9DKC

  • PubMed Abstract: 

    Hyperuricemia is a condition when uric acid, a waste product of purine metabolism, accumulates in the blood. Untreated hyperuricemia can lead to crystal formation of monosodium urate in the joints, causing a painful inflammatory disease known as gout. These conditions are associated with many other diseases and affect a significant and increasing proportion of the population. The human urate transporter 1 (URAT1) is responsible for the reabsorption of ~90% of uric acid in the kidneys back into the blood, making it a primary target for treating hyperuricemia and gout. Despite decades of research and development, clinically available URAT1 inhibitors have limitations because the molecular basis of URAT1 inhibition by gout drugs remains unknown. Here we present cryo-electron microscopy structures of URAT1 alone and in complex with three clinically relevant inhibitors: benzbromarone, lesinurad, and the recently developed compound TD-3. Together with functional experiments and molecular dynamics simulations, we reveal that these inhibitors bind selectively to URAT1 in inward-open states. Furthermore, we discover differences in the inhibitor-dependent URAT1 conformations as well as interaction networks, which contribute to drug specificity. Our findings illuminate a general theme for URAT1 inhibition, paving the way for the design of next-generation URAT1 inhibitors in the treatment of gout and hyperuricemia.


  • Organizational Affiliation
    • Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
URAT1518Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96S37 (Homo sapiens)
Explore Q96S37 
Go to UniProtKB:  Q96S37
PHAROS:  Q96S37
GTEx:  ENSG00000197891 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96S37
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A45
Query on A1A45

Download Ideal Coordinates CCD File 
B [auth A]2-({1-[(4-bromonaphthalen-1-yl)methyl]-1H-imidazo[4,5-b]pyridin-2-yl}sulfanyl)-2-methylpropanoic acid
C21 H18 Br N3 O2 S
VKHXJKYGFGXZSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21
RECONSTRUCTIONcryoSPARC4.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release