6CYI

Grp94 N-domain bound to NEOCA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75658 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

NECA derivatives exploit the paralog-specific properties of the site 3 side pocket of Grp94, the endoplasmic reticulum Hsp90.

Huck, J.D.Que, N.L.S.Immormino, R.M.Shrestha, L.Taldone, T.Chiosis, G.Gewirth, D.T.

(2019) J.Biol.Chem. 294: 16010-16019

  • DOI: 10.1074/jbc.RA119.009960
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The hsp90 chaperones govern the function of essential client proteins critical to normal cell function as well as cancer initiation and progression. Hsp90 activity is driven by ATP, which binds to the N-terminal domain (NTD) and induces large conform ...

    The hsp90 chaperones govern the function of essential client proteins critical to normal cell function as well as cancer initiation and progression. Hsp90 activity is driven by ATP, which binds to the N-terminal domain (NTD) and induces large conformational changes that are required for client maturation. Inhibitors targeting the ATP binding pocket of the NTD have anticancer effects, but most bind with similar affinity to cytosolic Hsp90α and β, endoplasmic reticulum Grp94, and mitochondrial Trap1, the four cellular hsp90 paralogs. Paralog-specific inhibitors may lead to drugs with fewer side effects.  The ATP binding pockets of the four paralogs are flanked by three side pockets, termed Sites 1, 2, and 3, which differ between the paralogs in their accessibility to inhibitors. Previous insights into the principles governing access to Sites 1 and 2 have resulted in the development of paralog-selective inhibitors targeting these sites, but the rules for selective targeting of Site 3 are less clear.  Previous work identified 5'N-ethylcarboxamido adenosine (NECA) as a Grp94-selective ligand.  Here, we use NECA and its derivatives to probe the properties of Site 3.  We found that derivatives that lengthen the 5' moiety of NECA improve selectivity for Grp94 over Hsp90α. Crystal structures reveal that the derivatives extend further into Site 3 of Grp94 compared to their parent compound and that selectivity is due to paralog-specific differences in ligand pose and ligand-induced conformational strain in the protein. These studies provide a structural basis for Grp94-selective inhibition using Site 3.


    Organizational Affiliation

    Memorial Sloan-Kettering Cancer Institute, United States.,Memorial Sloan Kettering, United States.,Hauptman-Woodward Medical Research Institute, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoplasmin
A
273Canis lupus familiarisMutation(s): 0 
Gene Names: HSP90B1 (GRP94, TRA1)
Find proteins for P41148 (Canis lupus familiaris)
Go to Gene View: HSP90B1
Go to UniProtKB:  P41148
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N5O
Query on N5O

Download SDF File 
Download CCD File 
A
5'-N-(2-HYDROXYL)ETHYL CARBOXYAMIDO ADENOSINE
(2S,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-N-(2-HYDROXYETHYL)TETRAHYDROFURAN-2-CARBOXAMIDE
C12 H16 N6 O5
YLPQAZPIFSHMAY-FLNNQWSLSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75658 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.204 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 89.055α = 90.00
b = 100.209β = 90.00
c = 63.433γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01CA186866
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA095130

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-10-23
    Type: Data collection, Database references
  • Version 1.2: 2019-10-30
    Type: Data collection, Database references
  • Version 1.3: 2019-11-13
    Type: Database references
  • Version 1.4: 2019-12-04
    Type: Author supporting evidence