4NH9 | pdb_00004nh9

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

• PDB DOI: https://doi.org/10.2210/pdb4NH9/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-11-04 Released: 2014-01-22 
• Deposition Author(s): Zuccola, H.J., Ernst, J.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 
  0.277 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.261 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Literature

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

• PubMed: 24332488 
• DOI: https://doi.org/10.1016/j.bmcl.2013.11.036
• Primary Citation 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.

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Organizational Affiliation: 
• Vertex Pharmaceuticals, Department of Chemistry and Drug Innovation, 11010 Torreyana Road, San Diego, CA 92121, United States. Electronic address: [e-mail].
Vertex Pharmaceuticals, Department of Biology, 11010 Torreyana Road, San Diego, CA 92121, United States.
Vertex Pharmaceuticals, Department of Protein Sciences, 130 Waverly Street, Cambridge, MA 02139, United States.
Vertex Pharmaceuticals, Department of Chemistry and Drug Innovation, 11010 Torreyana Road, San Diego, CA 92121, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.49 kDa 
• Atom Count: 1,704 
• Modeled Residue Count: 214 
• Deposited Residue Count: 273 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmin	A	273	Homo sapiens	Mutation(s): 0  Gene Names: HSP90B1, GRP94, TRA1 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P14625 (Homo sapiens) Explore P14625  Go to UniProtKB:  P14625
PHAROS:  P14625 GTEx:  ENSG00000166598

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2LC	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 GAGDTKJJVCLACJ-ZDUSSCGKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2LC	BindingDB:  4NH9	Ki: 375 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free:  0.277 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.261 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.102	α = 90
b = 101.194	β = 90
c = 63.497	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-22 
Deposition Author(s): Zuccola, H.J., Ernst, J.T.

Revision History  

• Version 1.0: 2014-01-22
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations