Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 28.8 kDa 
• Atom Count: 2,188 
• Modelled Residue Count: 246 
• Deposited Residue Count: 246 
• Unique protein chains: 1

 6CHW

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

• PDB DOI: 10.2210/pdb6CHW/pdb

• Classification: nuclear protein/antagonist
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-02-23 Released: 2018-03-21 
• Deposition Author(s): Larsen, N.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.257 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

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

• PubMed: 29991605 
• DOI: 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 .

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Organizational Affiliation: 

H3 Biomedicine, Inc., Cambridge, Massachusetts. [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A	246	Homo sapiens	Mutation(s): 3  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F3D	B [auth A]	4-[(2-{4-[(1E)-1-(1H-indazol-5-yl)-2-phenylbut-1-en-1-yl]phenoxy}ethyl)amino]-N,N-dimethylbutanamide C31 H36 N4 O2 MWRRXSSGLMVYRJ-CCFHIKDMSA-N
DMS	F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 58.735	α = 90
b = 58.735	β = 90
c = 274.814	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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