Crystal structure of human Trap1 with PU-H71

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

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Development of a Mitochondria-Targeted Hsp90 Inhibitor Based on the Crystal Structures of Human TRAP1

Lee, C.Park, H.K.Jeong, H.Lim, J.Lee, A.J.Cheon, K.Y.Kim, C.S.Thomas, A.P.Bae, B.Kim, N.D.Kim, S.H.Suh, P.G.Ryu, J.H.Kang, B.H.

(2015) J Am Chem Soc 137: 4358-4367

  • DOI: https://doi.org/10.1021/ja511893n
  • Primary Citation of Related Structures:  
    4Z1F, 4Z1G, 4Z1H, 4Z1I

  • PubMed Abstract: 

    The mitochondrial pool of Hsp90 and its mitochondrial paralogue, TRAP1, suppresses cell death and reprograms energy metabolism in cancer cells; therefore, Hsp90 and TRAP1 have been suggested as target proteins for anticancer drug development. Here, we report that the actual target protein in cancer cell mitochondria is TRAP1, and current Hsp90 inhibitors cannot effectively inactivate TRAP1 because of their insufficient accumulation in the mitochondria. To develop mitochondrial TRAP1 inhibitors, we determined the crystal structures of human TRAP1 complexed with Hsp90 inhibitors. The isopropyl amine of the Hsp90 inhibitor PU-H71 was replaced with the mitochondria-targeting moiety triphenylphosphonium to produce SMTIN-P01. SMTIN-P01 showed a different mode of action from the nontargeted PU-H71, as well as much improved cytotoxicity to cancer cells. In addition, we determined the structure of a TRAP1-adenylyl-imidodiphosphate (AMP-PNP) complex. On the basis of comparative analysis of TRAP1 structures, we propose a molecular mechanism of ATP hydrolysis that is crucial for chaperone function.

  • Organizational Affiliation

    ∥New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 701-310, Korea.

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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on H71

Download Ideal Coordinates CCD File 
C18 H21 I N6 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
H71 BindingDB:  4Z1F IC50: min: 205, max: 675 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.223α = 90
b = 69.223β = 90
c = 252.522γ = 90
Software Package:
Software NamePurpose
HKL-2000data processing
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-22
    Type: Initial release