6ASP

Structure of Grp94 with methyl 3-chloro-2-(2-(1-(2-ethoxybenzyl)-1 H-imidazol-2-yl)ethyl)-4,6-dihydroxybenzoate, a Grp94-selective inhibitor and promising therapeutic lead for treating myocilin-associated glaucoma


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.696 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Trifunctional High-Throughput Screen Identifies Promising Scaffold To Inhibit Grp94 and Treat Myocilin-Associated Glaucoma.

Huard, D.J.E.Crowley, V.M.Du, Y.Cordova, R.A.Sun, Z.Tomlin, M.O.Dickey, C.A.Koren, J.Blair, L.Fu, H.Blagg, B.S.J.Lieberman, R.L.

(2018) ACS Chem. Biol. 13: 933-941

  • DOI: 10.1021/acschembio.7b01083
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Gain-of-function mutations within the olfactomedin (OLF) domain of myocilin result in its toxic intracellular accumulation and hasten the onset of open-angle glaucoma. The absence of myocilin does not cause disease; therefore, strategies aimed at eli ...

    Gain-of-function mutations within the olfactomedin (OLF) domain of myocilin result in its toxic intracellular accumulation and hasten the onset of open-angle glaucoma. The absence of myocilin does not cause disease; therefore, strategies aimed at eliminating myocilin could lead to a successful glaucoma treatment. The endoplasmic reticulum Hsp90 paralog Grp94 accelerates OLF aggregation. Knockdown or pharmacological inhibition of Grp94 in cells facilitates clearance of mutant myocilin via a non-proteasomal pathway. Here, we expanded our support for targeting Grp94 over cytosolic paralogs Hsp90α and Hsp90β. We then developed a high-throughput screening assay to identify new chemical matter capable of disrupting the Grp94/OLF interaction. When applied to a blind, focused library of 17 Hsp90 inhibitors, our miniaturized single-read in vitro thioflavin T -based kinetics aggregation assay exclusively identified compounds that target the chaperone N-terminal nucleotide binding site. In follow up studies, one compound (2) decreased the extent of co-aggregation of Grp94 with OLF in a dose-dependent manner in vitro, and enabled clearance of the aggregation-prone full-length myocilin variant I477N in cells without inducing the heat shock response or causing cytotoxicity. Comparison of the co-crystal structure of compound 2 and another non-selective hit in complex with the N-terminal domain of Grp94 reveals a docking mode tailored to Grp94 and explains its selectivity. A new lead compound has been identified, supporting a targeted chemical biology assay approach to develop a protein degradation-based therapy for myocilin-associated glaucoma by selectively inhibiting Grp94.


    Organizational Affiliation

    School of Chemistry & Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoplasmin
A, B
233Canis 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
V2C
Query on V2C

Download SDF File 
Download CCD File 
A, B
methyl 3-chloro-2-(2-(1-(2-ethoxybenzyl)-1 H-imidazol-2-yl)ethyl)-4,6-dihydroxybenzoate
C22 H23 Cl N2 O5
ZPXKRKAPYWMXER-UHFFFAOYSA-N
 Ligand Interaction
P33
Query on P33

Download SDF File 
Download CCD File 
A, B
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
HEPTAETHYLENE GLYCOL, PEG330
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.696 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.661α = 90.00
b = 84.772β = 90.00
c = 96.013γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
PHASERphasing
PHENIXrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-05-02
    Type: Data collection, Database references
  • Version 1.2: 2019-04-17
    Type: Author supporting evidence, Data collection