4ASG

The structure of modified benzoquinone ansamycins bound to yeast N- terminal Hsp90


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Synthesis of 19-Substituted Geldanamycins with Altered Conformations and Their Binding to Heat Shock Protein Hsp90.

Kitson, R.R.A.Chang, C.Xiong, R.Williams, H.E.L.Davis, A.L.Lewis, W.Dehn, D.L.Siegel, D.Roe, S.M.Prodromou, C.Ross, D.Moody, C.J.

(2013) Nat Chem 5: 307

  • DOI: 10.1038/nchem.1596
  • Primary Citation of Related Structures:  
    4ASA, 4ASB, 4AS9, 4ASF, 4ASG

  • PubMed Abstract: 
  • The benzoquinone ansamycin geldanamycin and its derivatives are inhibitors of heat shock protein Hsp90, an emerging target for novel therapeutic agents both in cancer and in neurodegeneration. However, the toxicity of these compounds to normal cells has been ascribed to reaction with thiol nucleophiles at the quinone 19-position ...

    The benzoquinone ansamycin geldanamycin and its derivatives are inhibitors of heat shock protein Hsp90, an emerging target for novel therapeutic agents both in cancer and in neurodegeneration. However, the toxicity of these compounds to normal cells has been ascribed to reaction with thiol nucleophiles at the quinone 19-position. We reasoned that blocking this position would ameliorate toxicity, and that it might also enforce a favourable conformational switch of the trans-amide group into the cis-form required for protein binding. Here, we report an efficient synthesis of such 19-substituted compounds and realization of our hypotheses. Protein crystallography established that the new compounds bind to Hsp90 with, as expected, a cis-amide conformation. Studies on Hsp90 inhibition in cells demonstrated the molecular signature of Hsp90 inhibitors: decreases in client proteins with compensatory increases in other heat shock proteins in both human breast cancer and dopaminergic neural cells, demonstrating their potential for use in the therapy of cancer or neurodegenerative diseases.


    Organizational Affiliation

    School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-DEPENDENT MOLECULAR CHAPERONE HSP82A220Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P02829 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02829 
Go to UniProtKB:  P02829
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
814 (Subject of Investigation/LOI)
Query on 814

Download Ideal Coordinates CCD File 
B [auth A][(3R,5S,6R,7R,11S,12Z,14E)-5,11,21-trimethoxy-3,7,9,15-tetramethyl-6-oxidanyl-16,20,22-tris(oxidanylidene)-19-phenyl-17-azabicyclo[16.3.1]docosa-1(21),8,12,14,18-pentaen-10-yl] carbamate
C35 H44 N2 O9
PYMOVVPUXVGPNQ-BRFDUPECSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.126α = 90
b = 74.126β = 90
c = 110.177γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2015-09-23
    Changes: Non-polymer description
  • Version 1.2: 2017-06-28
    Changes: Data collection