Identification of novel HSP90/isoform selective inhibitors using structure-based drug design. Demonstration of potential utility in treating CNS disorders such as Huntington's disease

Experimental Data Snapshot

  • Resolution: 1.93 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Identification of Novel HSP90 alpha / beta Isoform Selective Inhibitors Using Structure-Based Drug Design. Demonstration of Potential Utility in Treating CNS Disorders such as Huntington's Disease.

Ernst, J.T.Neubert, T.Liu, M.Sperry, S.Zuccola, H.Turnbull, A.Fleck, B.Kargo, W.Woody, L.Chiang, P.Tran, D.Chen, W.Snyder, P.Alcacio, T.Nezami, A.Reynolds, J.Alvi, K.Goulet, L.Stamos, D.

(2014) J Med Chem 57: 3382-3400

  • DOI: https://doi.org/10.1021/jm500042s
  • Primary Citation of Related Structures:  
    4O04, 4O05, 4O07, 4O09, 4O0B

  • PubMed Abstract: 

    A structure-based drug design strategy was used to optimize a novel benzolactam series of HSP90α/β inhibitors to achieve >1000-fold selectivity versus the HSP90 endoplasmic reticulum and mitochondrial isoforms (GRP94 and TRAP1, respectively). Selective HSP90α/β inhibitors were found to be equipotent to pan-HSP90 inhibitors in promoting the clearance of mutant huntingtin protein (mHtt) in vitro, however with less cellular toxicity. Improved tolerability profiles may enable the use of HSP90α/β selective inhibitors in treating chronic neurodegenerative indications such as Huntington's disease (HD). A potent, selective, orally available HSP90α/β inhibitor was identified (compound 31) that crosses the blood-brain barrier. Compound 31 demonstrated proof of concept by successfully reducing brain Htt levels following oral dosing in rats.

  • Organizational Affiliation

    Vertex Pharmaceuticals , 11010 Torreyana Road, San Diego, California 92121, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alpha233Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens)
Explore P07900 
Go to UniProtKB:  P07900
PHAROS:  P07900
GTEx:  ENSG00000080824 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07900
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2QA

Download Ideal Coordinates CCD File 
B [auth A]8-cyclopentyl-6-(3,6,6-trimethyl-4-oxo-4,5,6,7-tetrahydro-1H-indol-1-yl)-3,4-dihydroisoquinolin-1(2H)-one
C25 H30 N2 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
2QA BindingDB:  4O0B Ki: min: 5, max: 5 (nM) from 2 assay(s)
IC50: min: 5, max: 24 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.93 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.4α = 90
b = 89.23β = 90
c = 97.37γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PROCESSdata collection
PROCESSdata reduction
PROCESSdata 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: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-05-07
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations