5UFW | pdb_00005ufw

Estrogen Receptor Alpha Ligand Binding Domain in Complex with OP1154

• PDB DOI: https://doi.org/10.2210/pdb5UFW/pdb

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


• Deposited: 2017-01-06 Released: 2018-01-10 
• Deposition Author(s): Fanning, S.W., Hodges-Gallagher, L., Myles, D.C., Sun, R., Fowler, C.E., Green, B.D., Harmon, C.L., Greene, G.L., Kushner, P.J.
• Funding Organization(s): Susan G. Komen Foundation, Ludwig Fund for Metastasis Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Specific stereochemistry of OP-1074 disrupts estrogen receptor alpha helix 12 and confers pure antiestrogenic activity.

Fanning, S.W., Hodges-Gallagher, L., Myles, D.C., Sun, R., Fowler, C.E., Plant, I.N., Green, B.D., Harmon, C.L., Greene, G.L., Kushner, P.J.

(2018) Nat Commun 9: 2368-2368

• PubMed: 29915250 
• DOI: https://doi.org/10.1038/s41467-018-04413-3
• Primary Citation Related Structures: 
  5UFW, 5UFX, 6C42


• PubMed Abstract: 
  

  Complex tissue-specific and cell-specific signaling by the estrogen receptor (ER) frequently leads to the development of resistance to endocrine therapy for breast cancer. Pure ER antagonists, which completely lack tissue-specific agonist activity, hold promise for preventing and treating endocrine resistance, however an absence of structural information hinders the development of novel candidates. Here we synthesize a small panel of benzopyrans with variable side chains to identify pure antiestrogens in a uterotrophic assay. We identify OP-1074 as a pure antiestrogen and a selective ER degrader (PA-SERD) that is efficacious in shrinking tumors in a tamoxifen-resistant xenograft model. Biochemical and crystal structure analyses reveal a structure activity relationship implicating the importance of a stereospecific methyl on the pyrrolidine side chain of OP-1074, particularly on helix 12.

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Organizational Affiliation: 
• Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA. [e-mail].
Olema Pharmaceuticals, San Francisco, CA, 94107, USA. [e-mail].
Olema Pharmaceuticals, San Francisco, CA, 94107, USA.
Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA.
Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.63 kDa 
• Atom Count: 4,490 
• Modeled Residue Count: 466 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	249	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
86V	C [auth A], D [auth B]	(2S)-3-(4-hydroxyphenyl)-4-methyl-2-(4-{2-[(3S)-3-methylpyrrolidin-1-yl]ethoxy}phenyl)-2H-1-benzopyran-7-ol C29 H31 N O4 KDVXAPCZVZMPMU-SLQAJWMNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.569	α = 90
b = 57.878	β = 102.91
c = 87.701	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	data reduction
PHENIX	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-10 
Deposition Author(s): Fanning, S.W., Hodges-Gallagher, L., Myles, D.C., Sun, R., Fowler, C.E., Green, B.D., Harmon, C.L., Greene, G.L., Kushner, P.J.

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Funding Organization	Location	Grant Number
Susan G. Komen Foundation	United States	PDF14301382
Ludwig Fund for Metastasis Research	United States	--

Revision History  

• Version 1.0: 2018-01-10
  Type: Initial release
  
• Version 1.1: 2018-06-27
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description