5AQZ

HSP72 with adenosine-derived inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5AQZ/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-09-22 Released: 2016-05-11 
• Deposition Author(s): Cheeseman, M.D., Westwood, I.M., Barbeau, O., Rowlands, M.G., Jones, A.M., Jeganathan, F., Burke, R., Dobson, S.E., Workman, P., Collins, I., van Montfort, R.L.M., Jones, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.221 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

Exploiting Protein Conformational Change to Optimize Adenosine-Derived Inhibitors of Hsp70.

Cheeseman, M.D., Westwood, I.M., Barbeau, O., Rowlands, M.G., Dobson, S., Jones, A.M., Jeganathan, F., Burke, R., Kadi, N., Workman, P., Collins, I., Van Montfort, R.L.M., Jones, K.

(2016) J Med Chem 59: 4625

• PubMed: 27119979 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b02001
• Primary Citation of Related Structures:  
  5AQZ, 5AR0


• PubMed Abstract: 
  

  HSP70 is a molecular chaperone and a key component of the heat-shock response. Because of its proposed importance in oncology, this protein has become a popular target for drug discovery, efforts which have as yet brought little success. This study demonstrates that adenosine-derived HSP70 inhibitors potentially bind to the protein with a novel mechanism of action, the stabilization by desolvation of an intramolecular salt-bridge which induces a conformational change in the protein, leading to high affinity ligands. We also demonstrate that through the application of this mechanism, adenosine-derived HSP70 inhibitors can be optimized in a rational manner.

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Organizational Affiliation: 

Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research , London SW7 3RP, U.K.

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: 43.75 kDa 
• Atom Count: 3,484 
• Modelled Residue Count: 390 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT SHOCK 70 KDA PROTEIN 1A	A	394	Homo sapiens	Mutation(s): 0  EC: 3.6.3.51
UniProt & NIH Common Fund Data Resources
Find proteins for P0DMV8 (Homo sapiens) Explore P0DMV8  Go to UniProtKB:  P0DMV8
GTEx:  ENSG00000204389

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SGV	B [auth A]	SANGIVAMYCIN C12 H15 N5 O5 OBZJZDHRXBKKTJ-JTFADIMSSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SGV	BindingDB:  5AQZ	Kd: min: 3236, max: 3300 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.221 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.938	α = 90
b = 89.504	β = 90
c = 96.92	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-11 
Deposition Author(s): Cheeseman, M.D., Westwood, I.M., Barbeau, O., Rowlands, M.G., Jones, A.M., Jeganathan, F., Burke, R., Dobson, S.E., Workman, P., Collins, I., van Montfort, R.L.M., Jones, K.

Revision History  

• Version 1.0: 2016-05-11
  Type: Initial release
  
• Version 1.1: 2016-06-08
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description