7RKE | pdb_00007rke

Estrogen Receptor Alpha Ligand Binding Domain Y537S in Complex with 4-(((2-chloro-5-phenylthieno[2,3-d]pyrimidin-4-yl)amino)methyl)phenol and GRIP Peptide

• PDB DOI: https://doi.org/10.2210/pdb7RKE/pdb

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


• Deposited: 2021-07-22 Released: 2022-06-22 
• Deposition Author(s): Joiner, C., Sammeta, V.K.R., Norris, J.D., McDonnell, D.P., Willson, T.M., Fanning, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.273 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

A New Chemotype of Chemically Tractable Nonsteroidal Estrogens Based on a Thieno[2,3- d ]pyrimidine Core.

Sammeta, V.R., Norris, J.D., Artham, S., Torrice, C.D., Byemerwa, J., Joiner, C., Fanning, S.W., McDonnell, D.P., Willson, T.M.

(2022) ACS Med Chem Lett 13: 1151-1158

• PubMed: 35859859 
• DOI: https://doi.org/10.1021/acsmedchemlett.2c00180
• Primary Citation Related Structures: 
  7RKE, 7T2X


• PubMed Abstract: 
  

  Despite continued interest in the development of nonsteroidal estrogens and antiestrogens, there are only a few chemotypes of estrogen receptor ligands. Using targeted screening in a ligand sensing assay, we identified a phenolic thieno[2,3- d ]pyrimidine with affinity for estrogen receptor α. An efficient three-step synthesis of the heterocyclic core and structure-guided optimization of the substituents resulted in a series of potent nonsteroidal estrogens. The chemical tractability of the thieno[2,3- d ]pyrimidine chemotype will support the design of new estrogen receptor ligands as therapeutic hormones and antihormones.

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Organizational Affiliation: 
• Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States.
Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States.
Department of Cancer Biology, Loyola University of Chicago Stritch School of Medicine, Maywood, Illinois 60611, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.17 kDa 
• Atom Count: 4,137 
• Modeled Residue Count: 466 
• Deposited Residue Count: 520 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	250	Homo sapiens	Mutation(s): 1  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2	C, D	10	Homo sapiens	Mutation(s): 0  Gene Names: NCOA2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
PHAROS:  Q15596 GTEx:  ENSG00000140396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5VP (Subject of Investigation/LOI)	E [auth A], F [auth B]	4-{[(2-chloro-5-phenylthieno[2,3-d]pyrimidin-4-yl)amino]methyl}phenol C19 H14 Cl N3 O S NNBAZKOESMUGEL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.273 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.027	α = 90
b = 83.943	β = 108.66
c = 58.662	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Joiner, C., Sammeta, V.K.R., Norris, J.D., McDonnell, D.P., Willson, T.M., Fanning, S.W.

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2022-08-03
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description