5VYY

Structure of human Hsp90-alpha bound to resorcinylic inhibitor BnIm


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

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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, 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alphaA256Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1HSP90AHSPC1HSPCA
EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens)
Explore P07900 
Go to UniProtKB:  P07900
PHAROS:  P07900
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9QY (Subject of Investigation/LOI)
Query on 9QY

Download Ideal Coordinates CCD File 
B [auth A]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]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9QY BindingDB:  5VYY Ki: 1800 (nM) from 1 assay(s)
Kd: min: 620, max: 1.31e+4 (nM) from 2 assay(s)
IC50: min: 1.31e+4, max: 1.40e+4 (nM) from 3 assay(s)
Binding MOAD:  5VYY Kd: 620 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.075α = 90
b = 92.055β = 90
c = 85.262γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

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 StatesR01-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