ERa_L536S (L536S/C381S/C471S,C530S) in complex with a tricyclic indole (compound 6)

Experimental Data Snapshot

  • Resolution: 1.74 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

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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

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor
A, B
252Homo sapiensMutation(s): 4 
Gene Names: ESR1ESRNR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
PHAROS:  P03372
GTEx:  ENSG00000091831 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LVH (Subject of Investigation/LOI)
Query on LVH

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(~{E})-3-[3,5-bis(fluoranyl)-4-[(1~{R},3~{R})-2-(2-fluoranyl-2-methyl-propyl)-1,3-dimethyl-4,9-dihydro-3~{H}-pyrido[3,4-b]indol-1-yl]phenyl]prop-2-enoic acid
C26 H27 F3 N2 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
LVH Binding MOAD:  6SUO IC50: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.74 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.18α = 90
b = 51.36β = 91.53
c = 82.78γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Derived calculations