7U8W

hTRAP1 with inhibitors

  • Classification: CHAPERONE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-03-09 Released: 2023-08-16 
  • Deposition Author(s): Deng, J., Matts, R., Peng, S.
  • Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


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Literature

Elucidation of novel TRAP1-Selective inhibitors that regulate mitochondrial processes.

Merfeld, T.Peng, S.Keegan, B.M.Crowley, V.M.Brackett, C.M.Gutierrez, A.McCann, N.R.Reynolds, T.S.Rhodes, M.C.Byrd, K.M.Deng, J.Matts, R.L.Blagg, B.S.J.

(2023) Eur J Med Chem 258: 115531-115531

  • DOI: https://doi.org/10.1016/j.ejmech.2023.115531
  • Primary Citation of Related Structures:  
    7U8U, 7U8V, 7U8W, 7U8X

  • PubMed Abstract: 

    Hsp90 isoform-selective inhibitors represent a new paradigm for novel anti-cancer drugs as each of the four isoforms have specific cellular localization, function, and client proteins. The mitochondrial isoform, TRAP1, is the least understood member of the Hsp90 family due to the lack of small molecule tools to study its biological function. Herein, we report novel TRAP1-selective inhibitors used to interrogate TRAP1's biological function along with co-crystal structures of such compounds bound to the N-terminus of TRAP1. Solution of the co-crystal structure allowed for a structure-based approach that resulted in compound 36, which is a 40 nM inhibitor with >250-fold TRAP1 selectivity over Grp94, the isoform with the highest structural similarity to TRAP1 within the N-terminal ATP binding site. Lead compounds 35 and 36 were found to selectively induce TRAP1 client protein degradation without inducing the heat shock response or disrupting Hsp90-cytosolic clients. They were also shown to inhibit OXPHOS, alter cellular metabolism towards glycolysis, disrupt TRAP1 tetramer stability, and disrupt the mitochondrial membrane potential.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Warren Family Research Center for Drug Discovery and Development, University of Notre Dame, Notre Dame, IN, 46556, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein 75 kDa, mitochondrial483Homo sapiensMutation(s): 0 
Gene Names: TRAP1HSP75
UniProt & NIH Common Fund Data Resources
Find proteins for Q12931 (Homo sapiens)
Explore Q12931 
Go to UniProtKB:  Q12931
PHAROS:  Q12931
GTEx:  ENSG00000126602 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12931
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KUC (Subject of Investigation/LOI)
Query on KUC

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
[5-(4-fluoro-2H-isoindole-2-carbonyl)-2-hydroxyphenyl](5-fluoro-2H-isoindol-2-yl)methanone
C24 H14 F2 N2 O3
NDSVVWMRIUKJHF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.07α = 90
b = 68.863β = 90
c = 182.545γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release