5WMT

Structure of GRP94 N-terminal Domain bound to resorcinylic inhibitor BnIm.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.748 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure Based Design of a Grp94-Selective Inhibitor: Exploiting a Key Residue in Grp94 To Optimize Paralog-Selective Binding.

Que, N.L.S.Crowley, V.M.Duerfeldt, A.S.Zhao, J.Kent, C.N.Blagg, B.S.J.Gewirth, D.T.

(2018) J. Med. Chem. 61: 2793-2805

  • DOI: 10.1021/acs.jmedchem.7b01608
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Grp94 and Hsp90, the ER and cytoplasmic hsp90 paralogs, share a conserved ATP-binding pocket that has been targeted for therapeutics. Paralog-selective inhibitors may lead to drugs with fewer side effects. Here, we analyzed 1 (BnIm), a benzyl imidazo ...

    Grp94 and Hsp90, the ER and cytoplasmic hsp90 paralogs, share a conserved ATP-binding pocket that has been targeted for therapeutics. Paralog-selective inhibitors may lead to drugs with fewer side effects. Here, we analyzed 1 (BnIm), a benzyl imidazole resorcinylic inhibitor, for its mode of binding. The structures of 1 bound to Hsp90 and Grp94 reveal large conformational changes in Grp94 but not Hsp90 that expose site 2, a binding pocket adjacent to the central ATP cavity that is ordinarily blocked. The Grp94:1 structure reveals a flipped pose of the resorcinylic scaffold that inserts into the exposed site 2. We exploited this flipped binding pose to develop a Grp94-selective derivative of 1. Our structural analysis shows that the ability of the ligand to insert its benzyl imidazole substituent into site 1, a different side pocket off the ATP binding cavity, is the key to exposing site 2 in Grp94.


    Organizational Affiliation

    Hauptman-Woodward Medical Research Institute , Buffalo , New York 14203 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoplasmin
A, B, C, D
236Canis lupus familiarisMutation(s): 0 
Gene Names: HSP90B1 (GRP94, TRA1)
Find proteins for P41148 (Canis lupus familiaris)
Go to Gene View: HSP90B1
Go to UniProtKB:  P41148
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
9QY
Query on 9QY

Download SDF File 
Download CCD File 
A, B, C, D
methyl 2-[2-(1-benzyl-1H-imidazol-2-yl)ethyl]-3-chloro-4,6-dihydroxybenzoate
resorcinylic inhibitor BnIm
C20 H19 Cl N2 O4
NCWIQXPFJORNJP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.748 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 94.412α = 90.00
b = 94.730β = 90.00
c = 179.250γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited States5R01 CA095130
National Institutes of Health/National Cancer InstituteUnited StatesP01 CA186866

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-04-25
    Type: Data collection, Database references