4IO8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


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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

  • DOI: 10.1371/journal.pone.0078443
  • Primary Citation of 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heat shock 70kDa protein 1A variantA382Homo sapiensMutation(s): 0 
Gene Names: HSPA1AHSP72HSPA1HSX70
UniProt & NIH Common Fund Data Resources
Find proteins for P0DMV8 (Homo sapiens)
Explore P0DMV8 
Go to UniProtKB:  P0DMV8
PHAROS:  P0DMV8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DMV8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3FD
Query on 3FD

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3FD BindingDB:  4IO8 Ki: 120 (nM) from 1 assay(s)
Kd: 300 (nM) from 1 assay(s)
IC50: min: 500, max: 1.04e+4 (nM) from 2 assay(s)
PDBBind:  4IO8 Kd: 228 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.68α = 90
b = 53.973β = 101.07
c = 70.796γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
BUSTERrefinement
XDSdata reduction
XSCALEdata 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: 2013-12-18
    Type: Initial release