7C04

Crystal structure of human Trap1 with DN203492


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Development of pyrazolo[3,4-d]pyrimidine-6-amine-based TRAP1 inhibitors that demonstrate in vivo anticancer activity in mouse xenograft models.

Kim, D.Kim, S.Y.Kim, D.Yoon, N.G.Yun, J.Hong, K.B.Lee, C.Lee, J.H.Kang, B.H.Kang, S.

(2020) Bioorg Chem 101: 103901-103901

  • DOI: 10.1016/j.bioorg.2020.103901
  • Primary Citation of Related Structures:  
    7C04, 7C05

  • PubMed Abstract: 
  • TNF Receptor Associated Protein 1 (TRAP1) is a mitochondrial paralog of Hsp90 related to the promotion of tumorigenesis in various cancers via maintaining mitochondrial integrity, reducing the production of reactive oxygen species, and reprogramming cellular metabolism ...

    TNF Receptor Associated Protein 1 (TRAP1) is a mitochondrial paralog of Hsp90 related to the promotion of tumorigenesis in various cancers via maintaining mitochondrial integrity, reducing the production of reactive oxygen species, and reprogramming cellular metabolism. Consequently, Hsp90 and TRAP1 have been targeted to develop cancer therapeutics. Herein, we report a series of pyrazolo[3,4-d]pyrimidine derivatives that are mitochondria-permeable TRAP1 inhibitors. Structure-based drug design guided the optimization of potency, leading to the identification of compounds 47 and 48 as potent TRAP1 and Hsp90 inhibitors with good metabolic and plasma stability as well as acceptable CYP and hERG inhibition. X-ray co-crystallization studies confirmed both 47 and 48 interact with the ATP binding pocket in the TRAP1 protein. Compounds 47 and 48 demonstrated excellent anticancer efficiency in various cancer cells, with limited toxicity over normal hepatocyte and prostate cells. Mouse PC3 xenograft studies showed 47 and 48 significantly reduced tumor growth.


    Organizational Affiliation

    College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, South Korea; Western Seoul Center, Korea Basic Science Institute, Seoul 03760, South Korea. Electronic address: sskang@ewha.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heat shock protein 75 kDa, mitochondrialA235Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FEU (Subject of Investigation/LOI)
Query on FEU

Download Ideal Coordinates CCD File 
B [auth A]4-chloranyl-1-[[2-methoxy-4-(trifluoromethyl)phenyl]methyl]pyrazolo[3,4-d]pyrimidin-6-amine
C14 H11 Cl F3 N5 O
CRNFGOLKBZYMGM-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FEU Binding MOAD:  7C04 IC50: 1983 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.405α = 90
b = 110.405β = 90
c = 59.445γ = 120
Software Package:
Software NamePurpose
HKL-2000data processing
PHENIXrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release