6SQ0

ERa_L536S (L536S/C381S/C471S,C530S) in complex with a bridged tetracyclic indole (compound 8)

• PDB DOI: https://doi.org/10.2210/pdb6SQ0/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-09-03 Released: 2019-10-30 
• Deposition Author(s): Breed, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.198 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Literature

Building Bridges in a Series of Estrogen Receptor Degraders: An Application of Metathesis in Medicinal Chemistry.

Scott, J.S., Breed, J., Carbajo, R.J., Davey, P.R., Greenwood, R., Huynh, H.K., Klinowska, T., Morrow, C.J., Moss, T.A., Polanski, R., Nissink, J.W.M., Varnes, J., Yang, B.

(2019) ACS Med Chem Lett 10: 1492-1497

• PubMed: 31620239 
• DOI: https://doi.org/10.1021/acsmedchemlett.9b00370
• Primary Citation of Related Structures:  
  6SQ0, 6SUO


• PubMed Abstract: 
  

  Herein we report the use of metathesis to construct a novel tetracyclic core in a series of estrogen receptor degraders. This improved the chemical stability, as assessed using an NMR-MS based assay, and gave a molecule with excellent physicochemical properties and pharmacokinetics in rat. X-ray crystallography established minimal perturbation of the bridged compounds relative to the unbridged analogues in the receptor binding pocket. Unfortunately, despite retaining excellent binding to ERα, this adversely affected the ability of the compounds to degrade the receptor.

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Organizational Affiliation: 

Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.25 kDa 
• Atom Count: 3,484 
• Modelled Residue Count: 439 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	252	Homo sapiens	Mutation(s): 4  Gene Names: ESR1, ESR, NR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
PHAROS:  P03372 GTEx:  ENSG00000091831

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LRQ (Subject of Investigation/LOI)	C [auth A], D [auth B]	Bridged tetracyclic indole C27 H27 F3 N2 O2 XPULPVUOUDRKNB-SAEWTEAUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.198 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.11	α = 90
b = 51.62	β = 90.98
c = 83.69	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Breed, J.

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2020-03-11
  Changes: Derived calculations
• Version 1.2: 2024-05-15
  Changes: Advisory, Data collection, Database references