6AOM

Structure of molecular chaperone Grp94 bound to selective inhibitor methyl 2-[2-(2-benzylphenyl)ethyl]-3-chloro-4,6-dihydroxybenzoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Second Generation Grp94-Selective Inhibitors Provide Opportunities for the Inhibition of Metastatic Cancer.

Crowley, V.M.Huard, D.J.E.Lieberman, R.L.Blagg, B.S.J.

(2017) Chemistry 23: 15775-15782

  • DOI: https://doi.org/10.1002/chem.201703398
  • Primary Citation of Related Structures:  
    6AOL, 6AOM

  • PubMed Abstract: 

    Glucose regulated protein 94 (Grp94) is the endoplasmic reticulum (ER) resident isoform of the 90 kDa heat shock protein (Hsp90) family and its inhibition represents a promising therapeutic target for the treatment of many diseases. Modification of the first generation cis-amide bioisostere imidazole to alter the angle between the resorcinol ring and the benzyl side chain via cis-amide replacements produced compounds with improved Grp94 affinity and selectivity. Structure-activity relationship studies led to the discovery of compound 30, which exhibits 540 nm affinity and 73-fold selectivity towards Grp94. Grp94 is responsible for the maturation and trafficking of proteins associated with cell signaling and motility, including select integrins. The Grp94-selective inhibitor 30 was shown to exhibit potent anti-migratory effects against multiple aggressive and metastatic cancers.


  • Organizational Affiliation

    Department of Medicinal Chemistry, The University of Kansas, 1251 Wescoe Hall Dr. Malott 4070, Lawrence, KS, 66045, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoplasmin
A, B
233Canis lupus familiarisMutation(s): 0 
Gene Names: HSP90B1GRP94TRA1
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VC5
Query on VC5

Download Ideal Coordinates CCD File 
K [auth A],
U [auth B]
methyl 2-[2-(2-benzylphenyl)ethyl]-3-chloro-4,6-dihydroxybenzoate
C23 H21 Cl O4
RHHYIPFMHURXDZ-UHFFFAOYSA-N
P33
Query on P33

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
O [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
P [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.454α = 90
b = 84.233β = 90
c = 94.966γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data 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: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary