5WMT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.2 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:  
    5VYY, 5WMT, 6CEO, 6C91, 6BAW

  • 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 imidazole resorcinylic inhibitor, for its mode of binding ...

    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

    Department of Structural Biology , University at Buffalo , Buffalo , New York 14203 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EndoplasminA, B, C, D236Canis lupus familiarisMutation(s): 0 
Gene Names: HSP90B1GRP94TRA1
UniProt
Find proteins for P41148 (Canis lupus familiaris)
Explore P41148 
Go to UniProtKB:  P41148
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9QY (Subject of Investigation/LOI)
Query on 9QY

Download Ideal Coordinates CCD File 
I [auth A], N [auth B], T [auth C], Y [auth D]methyl 2-[2-(1-benzyl-1H-imidazol-2-yl)ethyl]-3-chloro-4,6-dihydroxybenzoate
C20 H19 Cl N2 O4
NCWIQXPFJORNJP-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , J [auth B] , K [auth B] , L [auth B] , O [auth C] , 
E [auth A],  F [auth A],  G [auth A],  H [auth A],  J [auth B],  K [auth B],  L [auth B],  O [auth C],  P [auth C],  Q [auth C],  R [auth C],  U [auth D],  V [auth D],  W [auth D],  X [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
M [auth B], S [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9QY BindingDB:  5WMT Ki: 440 (nM) from 1 assay(s)
Kd: 1380 (nM) from 1 assay(s)
IC50: 1100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.412α = 90
b = 94.73β = 90
c = 179.25γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5R01 CA095130
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01 CA186866

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence