5IN9 | pdb_00005in9

Crystal structure of Grp94 bound to methyl 3-chloro-2-(2-(1-((5-chlorofuran-2-yl)methyl)-1H-imidazol-2-yl)ethyl)-4,6-dihydroxybenzoate, an inhibitor based on the BnIm and Radamide scaffolds.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Development of Glucose Regulated Protein 94-Selective Inhibitors Based on the BnIm and Radamide Scaffold.

Crowley, V.M.Khandelwal, A.Mishra, S.Stothert, A.R.Huard, D.J.Zhao, J.Muth, A.Duerfeldt, A.S.Kizziah, J.L.Lieberman, R.L.Dickey, C.A.Blagg, B.S.

(2016) J Med Chem 59: 3471-3488

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b00085
  • Primary Citation Related Structures: 
    5IN9

  • PubMed Abstract: 

    Glucose regulated protein 94 (Grp94) is the endoplasmic reticulum resident of the heat shock protein 90 kDa (Hsp90) family of molecular chaperones. Grp94 associates with many proteins involved in cell adhesion and signaling, including integrins, Toll-like receptors, immunoglobulins, and mutant myocilin. Grp94 has been implicated as a target for several therapeutic areas including glaucoma, cancer metastasis, and multiple myeloma. While 85% identical to other Hsp90 isoforms, the N-terminal ATP-binding site of Grp94 possesses a unique hydrophobic pocket that was used to design isoform-selective inhibitors. Incorporation of a cis-amide bioisostere into the radamide scaffold led to development of the original Grp94-selective inhibitor, BnIm. Structure-activity relationship studies have now been performed on the aryl side chain of BnIm, which resulted in improved analogues that exhibit better potency and selectivity for Grp94. These analogues also manifest superior antimigratory activity in a metastasis model as well as enhanced mutant myocilin degradation in a glaucoma model compared to BnIm.


  • Organizational Affiliation
    • Department of Medicinal Chemistry, The University of Kansas , 1251 Wescoe Hall Drive, Malott Hall 4070, Lawrence, Kansas 66045-7563, United States.

Macromolecule Content 

  • Total Structure Weight: 54.55 kDa 
  • Atom Count: 3,672 
  • Modeled Residue Count: 435 
  • 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
6C0

Query on 6C0



Download:Ideal Coordinates CCD File
L [auth A],
R [auth B]
methyl 3-chloro-2-(2-{1-[(5-chlorofuran-2-yl)methyl]-1H-imidazol-2-yl}ethyl)-4,6-dihydroxybenzoate
C18 H16 Cl2 N2 O5
HIYQDMHJUHUDDN-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
C [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [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],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.02α = 90
b = 65.65β = 92.91
c = 95.86γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata 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: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Data collection
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description