6C91

Structure of GRP94 with a resorcinylic inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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, 6BAW, 6C91, 6CEO

  • 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
EndoplasminB, A [auth C]236Canis 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
EQD (Subject of Investigation/LOI)
Query on EQD

Download Ideal Coordinates CCD File 
E [auth C], M [auth B]5-[2-(1-benzyl-1H-imidazol-2-yl)ethyl]-4,6-dichlorobenzene-1,3-diol
C18 H16 Cl2 N2 O2
VJODJXMSNZNVSM-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C, D [auth C], I [auth B], J [auth B], K [auth B], L [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth C] , G [auth C] , H [auth C] , N [auth B] , O [auth B] , P [auth B] , Q [auth B] , R [auth B] , 
F [auth C], G [auth C], H [auth C], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EQD BindingDB:  6C91 Ki: 440 (nM) from 1 assay(s)
IC50: 1200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.05α = 90
b = 95.05β = 90
c = 178.589γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data 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 Cancer Institute (NIH/NCI)United StatesP01-CA186866
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01-CA095130

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: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence