5TTZ | pdb_00005ttz

Crystal structure of Grp94 bound to isoform-selective inhibitor methyl 2-(2-(1-(4-bromobenzyl)-1H-imidazol-2-yl)ethyl)-3-chloro-4,6-dihydroxybenzoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 
    0.285 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Isoform-selective Hsp90 inhibition rescues model of hereditary open-angle glaucoma.

Stothert, A.R.Suntharalingam, A.Tang, X.Crowley, V.M.Mishra, S.J.Webster, J.M.Nordhues, B.A.Huard, D.J.E.Passaglia, C.L.Lieberman, R.L.Blagg, B.S.J.Blair, L.J.Koren, J.Dickey, C.A.

(2017) Sci Rep 7: 17951-17951

  • DOI: https://doi.org/10.1038/s41598-017-18344-4
  • Primary Citation Related Structures: 
    5TTZ

  • PubMed Abstract: 

    The heat shock protein 90 (Hsp90) family of molecular chaperones regulates protein homeostasis, folding, and degradation. The ER-resident Hsp90 isoform, glucose-regulated protein 94 (Grp94), promotes the aggregation of mutant forms of myocilin, a protein associated with primary open-angle glaucoma. While inhibition of Grp94 promotes the degradation of mutant myocilin in vitro, to date no Grp94-selective inhibitors have been investigated in vivo. Here, a Grp94-selective inhibitor facilitated mutant myocilin degradation and rescued phenotypes in a transgenic mouse model of hereditary primary open-angle glaucoma. Ocular toxicities previously associated with pan-Hsp90 inhibitors were not evident with our Grp94-selective inhibitor, 4-Br-BnIm. Our study suggests that selective inhibition of a distinct Hsp90 family member holds translational promise for ocular and other diseases associated with cell stress and protein misfolding.


  • Organizational Affiliation
    • Department of Molecular Medicine and Byrd Alzheimer's Research Institute, University of South Florida, Tampa, FL, 33613, USA.

Macromolecule Content 

  • Total Structure Weight: 54.11 kDa 
  • Atom Count: 3,454 
  • Modeled Residue Count: 428 
  • 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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7KY

Query on 7KY



Download:Ideal Coordinates CCD File
C [auth A],
E [auth B]
methyl 2-(2-{1-[(4-bromophenyl)methyl]-1H-imidazol-2-yl}ethyl)-3-chloro-4,6-dihydroxybenzoate
C20 H18 Br Cl N2 O4
FHDUIAYTJZAXNW-UHFFFAOYSA-N
PE4

Query on PE4



Download:Ideal Coordinates CCD File
H [auth B]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
F [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
G [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
D [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free:  0.285 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.237α = 90
b = 84.42β = 90
c = 95.473γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesR01EY021205

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-04
    Changes: Advisory, Data collection, Database references, Refinement description