Estrogen Receptor Alpha Y537S covalently bound to antagonist H3B-5942.

Experimental Data Snapshot

  • Resolution: 1.89 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Discovery of Selective Estrogen Receptor Covalent Antagonists for the Treatment of ER alphaWTand ER alphaMUTBreast Cancer.

Puyang, X.Furman, C.Zheng, G.Z.Wu, Z.J.Banka, D.Aithal, K.Agoulnik, S.Bolduc, D.M.Buonamici, S.Caleb, B.Das, S.Eckley, S.Fekkes, P.Hao, M.H.Hart, A.Houtman, R.Irwin, S.Joshi, J.J.Karr, C.Kim, A.Kumar, N.Kumar, P.Kuznetsov, G.Lai, W.G.Larsen, N.Mackenzie, C.Martin, L.A.Melchers, D.Moriarty, A.Nguyen, T.V.Norris, J.O'Shea, M.Pancholi, S.Prajapati, S.Rajagopalan, S.Reynolds, D.J.Rimkunas, V.Rioux, N.Ribas, R.Siu, A.Sivakumar, S.Subramanian, V.Thomas, M.Vaillancourt, F.H.Wang, J.Wardell, S.Wick, M.J.Yao, S.Yu, L.Warmuth, M.Smith, P.G.Zhu, P.Korpal, M.

(2018) Cancer Discov 8: 1176-1193

  • DOI: https://doi.org/10.1158/2159-8290.CD-17-1229
  • Primary Citation of Related Structures:  
    6CHW, 6CHZ

  • PubMed Abstract: 

    Mutations in estrogen receptor alpha (ERα) that confer resistance to existing classes of endocrine therapies are detected in up to 30% of patients who have relapsed during endocrine treatments. Because a significant proportion of therapy-resistant breast cancer metastases continue to be dependent on ERα signaling, there remains a critical need to develop the next generation of ERα antagonists that can overcome aberrant ERα activity. Through our drug-discovery efforts, we identified H3B-5942, which covalently inactivates both wild-type and mutant ERα by targeting Cys530 and enforcing a unique antagonist conformation. H3B-5942 belongs to a class of ERα antagonists referred to as selective estrogen receptor covalent antagonists (SERCA). In vitro comparisons of H3B-5942 with standard-of-care (SoC) and experimental agents confirmed increased antagonist activity across a panel of ERα WT and ERα MUT cell lines. In vivo , H3B-5942 demonstrated significant single-agent antitumor activity in xenograft models representing ERα WT and ERα Y537S breast cancer that was superior to fulvestrant. Lastly, H3B-5942 potency can be further improved in combination with CDK4/6 or mTOR inhibitors in both ERα WT and ERα MUT cell lines and/or tumor models. In summary, H3B-5942 belongs to a class of orally available ERα covalent antagonists with an improved profile over SoCs. Significance: Nearly 30% of endocrine therapy-resistant breast cancer metastases harbor constitutively activating mutations in ERα. SERCA H3B-5942 engages C530 of both ERα WT and ERα MUT , promotes a unique antagonist conformation, and demonstrates improved in vitro and in vivo activity over SoC agents. Importantly, single-agent efficacy can be further enhanced by combining with CDK4/6 or mTOR inhibitors. Cancer Discov; 8(9); 1176-93. ©2018 AACR. This article is highlighted in the In This Issue feature, p. 1047 .

  • Organizational Affiliation

    H3 Biomedicine, Inc., Cambridge, Massachusetts.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor246Homo sapiensMutation(s): 3 
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
Experimental Data & Validation

Experimental Data

  • Resolution: 1.89 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.735α = 90
b = 58.735β = 90
c = 274.814γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2018-03-21 
  • Deposition Author(s): Larsen, N.A.

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-07-25
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.3: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.4: 2020-02-26
    Changes: Derived calculations