8Z3J | pdb_00008z3j

Benzbromarone interferes with the interaction between Hsp90 and Aha1 by interacting with both of them


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 
    0.199 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Benzbromarone interferes with the interaction between Hsp90 and Aha1 by interacting with both of them.

Zhong, Y.Shi, L.Xu, Z.Gao, J.Ma, Q.Gao, T.Tang, J.Xiong, M.Xu, Y.Dai, H.Zhou, H.Zhang, N.Zhou, C.

(2025) Commun Biol 8: 761-761

  • DOI: https://doi.org/10.1038/s42003-025-08189-3
  • Primary Citation Related Structures: 
    8Z3H, 8Z3J

  • PubMed Abstract: 

    Aha1 is one of the well-known co-chaperones of Hsp90. However, the action mode of Aha1 has not been fully elucidated yet, and the binding mode of Aha1's C-terminal domain (Aha1-CTD) to Hsp90 is still under discussion. Meanwhile, since both Hsp90 and Aha1 contribute to tumorigenesis through controlling the homeostasis of onco-proteins, Hsp90-Aha1 system might serve as a target for anti-tumor drug development. A few of active compounds towards Hsp90-Aha1 system have been reported during the past years, but no compound binding pocket in Aha1 was pictured yet. Here in this manuscript, by using the discovered dual-modulator Benzbromarone as the probe, the pocket in Aha1 responsible for compound recognition is defined. Interestingly, as shown by the cryo-EM structures of Hsp90:Aha1 system, it is the same pocket that is involved in the in vitro interaction between Aha1-CTD and Hsp90-MD. Besides, Benzbromarone's binding to Hsp90-NTD also exhibits unique structural features. Not surprisingly, due to the interference with the Hsp90 machinery, Benzbromarone could down-regulate the ATPase activity of the chaperone. Finally, according to the cellular-based experimental data, Benzbromarone has been shown to exhibit cytotoxicity against multiple cancer cell types, at least in part, through its modulation of the Hsp90 system.


  • Organizational Affiliation
    • State Key Laboratory of Chemical Biology, Analytical Research Center for Organic and Biological Molecules, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 15.61 kDa 
  • Atom Count: 1,170 
  • Modeled Residue Count: 132 
  • Deposited Residue Count: 132 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Activator of 90 kDa heat shock protein ATPase homolog 1132Homo sapiensMutation(s): 0 
Gene Names: AHSA1C14orf3HSPC322
UniProt & NIH Common Fund Data Resources
Find proteins for O95433 (Homo sapiens)
Explore O95433 
Go to UniProtKB:  O95433
PHAROS:  O95433
GTEx:  ENSG00000100591 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95433
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: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free:  0.199 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.216α = 90
b = 66.802β = 90
c = 68.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Database references