4IO8 | pdb_00004io8

Crystal structure of human HSP70 complexed with 4-{(2R,3S,4R)-5-[(R)-6-Amino-8-(3,4-dichloro-benzylamino)-purin-9-yl]-3,4-dihydroxy-tetrahydro-furan-2-ylmethoxymethyl}-benzonitrile

• PDB DOI: https://doi.org/10.2210/pdb4IO8/pdb

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


• Deposited: 2013-01-07 Released: 2013-12-18 
• Deposition Author(s): Musil, D., Scholz, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.222 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Functional analysis of hsp70 inhibitors.

Schlecht, R., Scholz, S.R., Dahmen, H., Wegener, A., Sirrenberg, C., Musil, D., Bomke, J., Eggenweiler, H.M., Mayer, M.P., Bukau, B.

(2013) PLoS One 8: e78443-e78443

• PubMed: 24265689 
• DOI: https://doi.org/10.1371/journal.pone.0078443
• Primary Citation Related Structures: 
  4IO8


• PubMed Abstract: 
  

  The molecular chaperones of the Hsp70 family have been recognized as targets for anti-cancer therapy. Since several paralogs of Hsp70 proteins exist in cytosol, endoplasmic reticulum and mitochondria, we investigated which isoform needs to be down-regulated for reducing viability of cancer cells. For two recently identified small molecule inhibitors, VER-155008 and 2-phenylethynesulfonamide (PES), which are proposed to target different sites in Hsp70s, we analyzed the molecular mode of action in vitro. We found that for significant reduction of viability of cancer cells simultaneous knockdown of heat-inducible Hsp70 (HSPA1) and constitutive Hsc70 (HSPA8) is necessary. The compound VER-155008, which binds to the nucleotide binding site of Hsp70, arrests the nucleotide binding domain (NBD) in a half-open conformation and thereby acts as ATP-competitive inhibitor that prevents allosteric control between NBD and substrate binding domain (SBD). Compound PES interacts with the SBD of Hsp70 in an unspecific, detergent-like fashion, under the conditions tested. None of the two inhibitors investigated was isoform-specific.

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Organizational Affiliation: 
• Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH-Alliance, Heidelberg, Germany.

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: 42.63 kDa 
• Atom Count: 3,085 
• Modeled Residue Count: 377 
• Deposited Residue Count: 382 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock 70kDa protein 1A variant	A	382	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0DMV8 (Homo sapiens) Explore P0DMV8  Go to UniProtKB:  P0DMV8
PHAROS:  P0DMV8 GTEx:  ENSG00000204389

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3FD	B [auth A]	4-[[(2R,3S,4R,5R)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile C25 H23 Cl2 N7 O4 ZXGGCBQORXDVTE-UMCMBGNQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.222 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.68	α = 90
b = 53.973	β = 101.07
c = 70.796	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-18 
Deposition Author(s): Musil, D., Scholz, S.

Revision History  

• Version 1.0: 2013-12-18
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description