Estrogen receptor mutant L536S

Experimental Data Snapshot

  • Resolution: 1.48 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Discovery of 6-(2,4-Dichlorophenyl)-5-[4-[(3S)-1-(3-fluoropropyl)pyrrolidin-3-yl]oxyphenyl]-8,9-dihydro-7H-benzo[7]annulene-2-carboxylic acid (SAR439859), a Potent and Selective Estrogen Receptor Degrader (SERD) for the Treatment of Estrogen-Receptor-Positive Breast Cancer.

El-Ahmad, Y.Tabart, M.Halley, F.Certal, V.Thompson, F.Filoche-Romme, B.Gruss-Leleu, F.Muller, C.Brollo, M.Fabien, L.Loyau, V.Bertin, L.Richepin, P.Pilorge, F.Desmazeau, P.Girardet, C.Beccari, S.Louboutin, A.Lebourg, G.Le-Roux, J.Terrier, C.Vallee, F.Steier, V.Mathieu, M.Rak, A.Abecassis, P.Y.Vicat, P.Benard, T.Bouaboula, M.Sun, F.Shomali, M.Hebert, A.Levit, M.Cheng, H.Courjaud, A.Ginesty, C.Perrault, C.Garcia-Echeverria, C.McCort, G.Schio, L.

(2020) J Med Chem 63: 512-528

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01293
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    More than 75% of breast cancers are estrogen receptor alpha (ERα) positive (ER+), and resistance to current hormone therapies occurs in one-third of ER+ patients. Tumor resistance is still ERα-dependent, but mutations usually confer constitutive activation to the hormone receptor, rendering ERα modulator drugs such as tamoxifen and aromatase inhibitors ineffective. Fulvestrant is a potent selective estrogen receptor degrader (SERD), which degrades the ERα receptor in drug-resistant tumors and has been approved for the treatment of hormone-receptor-positive metastatic breast cancer following antiestrogen therapy. However, fulvestrant shows poor pharmacokinetic properties in human, low solubility, weak permeation, and high metabolism, limiting its administration to inconvenient intramuscular injections. This Drug Annotation describes the identification and optimization of a new series of potent orally available SERDs, which led to the discovery of 6-(2,4-dichlorophenyl)-5-[4-[(3 S )-1-(3-fluoropropyl)pyrrolidin-3-yl]oxyphenyl]-8,9-dihydro-7 H -benzo[7]annulene-2-carboxylic acid ( 43d ), showing promising antitumor activity in breast cancer mice xenograft models and whose properties warranted clinical evaluation.

  • Organizational Affiliation

    Oncology , Sanofi , 640 Memorial Drive , Cambridge , Massachusetts 02139 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor
A, B
260Homo sapiensMutation(s): 1 
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
L5B (Subject of Investigation/LOI)
Query on L5B

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
6-(2,4-dichlorophenyl)-5-[4-[(3~{S})-1-(3-fluoranylpropyl)pyrrolidin-3-yl]oxyphenyl]-8,9-dihydro-7~{H}-benzo[7]annulene-2-carboxylic acid
C31 H30 Cl2 F N O3
Binding Affinity Annotations 
IDSourceBinding Affinity
L5B BindingDB:  6SBO IC50: min: 15, max: 389 (nM) from 3 assay(s)
EC50: 0.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.48 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.43α = 90
b = 57.71β = 103.13
c = 87.8γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Database references