6ASP | pdb_00006asp

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: 2.70 Å
  • R-Value Free: 
    0.238 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6ASP

Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acschembio.7b01083
  • Primary Citation Related Structures: 
    6ASP, 6ASQ

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 58.97 kDa 
  • Atom Count: 3,579 
  • Modeled Residue Count: 432 
  • Deposited Residue Count: 466 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endoplasmin
A, B
233Canis lupus familiarisMutation(s): 0 
Gene Names: HSP90B1GRP94TRA1
EC: 3.6.4
UniProt
Find proteins for P41148 (Canis lupus familiaris)
Explore P41148 
Go to UniProtKB:  P41148
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41148
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V2C

Query on V2C



Download:Ideal Coordinates CCD File
Q [auth A],
W [auth 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
P33

Query on P33



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
P [auth A],
V [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.238 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.661α = 90
b = 84.772β = 90
c = 96.013γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data 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: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary