6AOL | pdb_00006aol

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

• PDB DOI: https://doi.org/10.2210/pdb6AOL/pdb

• Classification: CHAPERONE/INHIBITOR
• Organism(s): Canis lupus familiaris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-08-16 Released: 2017-10-11 
• Deposition Author(s): Lieberman, R.L., Huard, D.J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 
  0.279 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

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

• PubMed: 28857290 
• DOI: https://doi.org/10.1002/chem.201703398
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, The University of Kansas, 1251 Wescoe Hall Dr. Malott 4070, Lawrence, KS, 66045, USA.
School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
Warren Family Research Center for Drug Discovery and Development, and Department of Chemistry & Biochemistry, University of Notre Dame, 305 McCourtney Hall, Notre Dame, IN, 46556, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 27.91 kDa 
• Atom Count: 1,780 
• Modeled Residue Count: 217 
• Deposited Residue Count: 233 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmin	A	233	Canis lupus familiaris	Mutation(s): 0  Gene Names: HSP90B1, GRP94, TRA1 EC: 3.6.4
UniProt
Find proteins for P41148 (Canis lupus familiaris) Explore P41148  Go to UniProtKB:  P41148

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VC1 (Subject of Investigation/LOI)	B [auth A]	methyl 3-chloro-2-(2-{2-[(4-fluorophenyl)methyl]phenyl}ethyl)-4,6-dihydroxybenzoate C23 H20 Cl F O4 IJGOZBLFBZMVDS-UHFFFAOYSA-N
P33	C [auth A], D [auth A], E [auth A], F [auth A]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free:  0.279 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.599	α = 90
b = 96.897	β = 90
c = 42.953	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Lieberman, R.L., Huard, D.J.E.

Revision History  

• 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