5Y3O

Structure of TRAP1 complexed with DN320


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Paralog Specificity Determines Subcellular Distribution, Action Mechanism, and Anticancer Activity of TRAP1 Inhibitors.

Park, H.K.Jeong, H.Ko, E.Lee, G.Lee, J.E.Lee, S.K.Lee, A.J.Im, J.Y.Hu, S.Kim, S.H.Lee, J.H.Lee, C.Kang, S.Kang, B.H.

(2017) J Med Chem 60: 7569-7578

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00978
  • Primary Citation of Related Structures:  
    5Y3N, 5Y3O

  • PubMed Abstract: 

    Although Hsp90 inhibitors can inhibit multiple tumorigenic pathways in cancer cells, their anticancer activity has been disappointingly modest. However, by forcing Hsp90 inhibitors into the mitochondria with mitochondrial delivery vehicles, they were converted into potent drugs targeting the mitochondrial Hsp90 paralog TRAP1. Here, to improve mitochondrial drug accumulation without using the mitochondrial delivery vehicle, we increased freely available drug concentrations in the cytoplasm by reducing the binding of the drugs to the abundant cytoplasmic Hsp90. After analyzing X-ray cocrystal structures, the purine ring of the Hsp90 inhibitor 2 (BIIB021) was modified to pyrazolopyrimidine scaffolds. One pyrazolopyrimidine, 12b (DN401), bound better to TRAP1 than to Hsp90, inactivated the mitochondrial TRAP1 in vivo, and it exhibited potent anticancer activity. Therefore, the rationale and feasible guidelines for developing 12b can potentially be exploited to design a potent TRAP1 inhibitor.


  • Organizational Affiliation

    Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST) , Ulsan 44919, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein 75 kDa, mitochondrial502Homo 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
8M9
Query on 8M9

Download Ideal Coordinates CCD File 
B [auth A]4-chloranyl-1-[(4-methoxy-3,5-dimethyl-pyridin-2-yl)methyl]pyrazolo[3,4-d]pyrimidin-6-amine
C14 H15 Cl N6 O
IKGRZHVFOMUXCQ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
8M9 BindingDB:  5Y3O IC50: 138 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.491α = 90
b = 69.491β = 90
c = 252.994γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references