Correlation between chemotype-dependent binding conformations of HSP90 alpha/beta and isoform selectivity

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

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Correlation between chemotype-dependent binding conformations of HSP90 alpha / beta and isoform selectivity-Implications for the structure-based design of HSP90 alpha / beta selective inhibitors for treating neurodegenerative diseases.

Ernst, J.T.Liu, M.Zuccola, H.Neubert, T.Beaumont, K.Turnbull, A.Kallel, A.Vought, B.Stamos, D.

(2014) Bioorg Med Chem Lett 24: 204-208

  • DOI: https://doi.org/10.1016/j.bmcl.2013.11.036
  • Primary Citation of Related Structures:  
    4NH7, 4NH8, 4NH9

  • PubMed Abstract: 

    HSP90 continues to be a target of interest for neurodegeneration indications. Selective knockdown of the HSP90 cytosolic isoforms α and β is sufficient to reduce mutant huntingtin protein levels in vitro. Chemotype-dependent binding conformations of HSP90α/β appear to strongly influence isoform selectivity. The rational design of HSP90α/β inhibitors selective versus the mitochondrial (TRAP1) and endoplasmic reticulum (GRP94) isoforms offers a potential mitigating strategy for mechanism-based toxicities. Better tolerated HSP90 inhibitors would be attractive for targeting chronic neurodegenerative diseases such as Huntington's disease.

  • Organizational Affiliation

    Vertex Pharmaceuticals, Department of Chemistry and Drug Innovation, 11010 Torreyana Road, San Diego, CA 92121, United States. Electronic address: Justin_Ernst@vrtx.com.

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 2LC

Download Ideal Coordinates CCD File 
B [auth A]2-fluoro-6-[(3S)-tetrahydrofuran-3-ylamino]-4-(3,6,6-trimethyl-4-oxo-4,5,6,7-tetrahydro-1H-indol-1-yl)benzamide
C22 H26 F N3 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
2LC Binding MOAD:  4NH8 Ki: 3 (nM) from 1 assay(s)
BindingDB:  4NH8 IC50: 30 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.87α = 90
b = 90.84β = 90
c = 99.04γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PROCESSdata reduction
PROCESSdata 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: 2014-01-15
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations