7C7C

Crystal structure of human TRAP1 with SJT104


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.236 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design and Synthesis of TRAP1 Selective Inhibitors: H-Bonding with Asn171 Residue in TRAP1 Increases Paralog Selectivity.

Yang, S.Yoon, N.G.Kim, D.Park, E.Kim, S.Y.Lee, J.H.Lee, C.Kang, B.H.Kang, S.

(2021) ACS Med Chem Lett 12: 1173-1180

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00213
  • Primary Citation of Related Structures:  
    7C7B, 7C7C

  • PubMed Abstract: 

    Tumor necrosis factor receptor-associated protein 1 (TRAP1) is overexpressed in the mitochondria of various cancer cells, reprograms cellular metabolism to enable cancer cells to adapt to harsh tumor environments. As inactivation of TRAP1 induces massive apoptosis in cancer cells in vitro and in vivo , the development of TRAP1-selective inhibitors has become an attractive approach. A series of purine-8-one and pyrrolo[2,3- d ]pyrimidine derivatives was developed based on TRAP1 structure and identified to be highly selective in vitro for TRAP1 over the paralogous enzymes, Hsp90α and Grp94. The TRAP1-selective inhibition strategy via utilization of the Asn171 residue of the ATP-lid was investigated using X-ray crystallography and molecular dynamics simulation studies. Among various synthesized potent TRAP1 inhibitors, 5f possessed a 65-fold selectivity over Hsp90α and a 13-fold selectivity over Grp94. Additionally, 6f had a half-maximal inhibitory concentration (IC 50 ) of 63.5 nM for TRAP1, with a 78-fold and 30-fold selectivity over Hsp90α and Grp94, respectively.


  • Organizational Affiliation

    College of Pharmacy, Ewha Womans University, Seoul 03760, Republic of 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FK0 (Subject of Investigation/LOI)
Query on FK0

Download Ideal Coordinates CCD File 
B [auth A]2-azanyl-9-[(4-bromanyl-2-fluoranyl-phenyl)methyl]-6-chloranyl-purin-8-ol
C12 H8 Br Cl F N5 O
CCUHAWKQXDIYIR-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FK0 BindingDB:  7C7C IC50: 58 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.236 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.543α = 90
b = 69.543β = 90
c = 251.327γ = 90
Software Package:
Software NamePurpose
HKL-2000data processing
PHENIXrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description