7RNM

Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with 2-(2-Chloro-5-phenylthieno[2,3-d]pyrimidin-4-yl)isoindolin-5-ol and GRIP Peptide

• PDB DOI: https://doi.org/10.2210/pdb7RNM/pdb

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


• Deposited: 2021-07-29 Released: 2022-08-03 
• 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: 1.90 Å
• R-Value Free: 0.221 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Structural Determinants of the Binding and Activation of Estrogen Receptor alpha by Phenolic Thieno[2,3-d]pyrimidines

Reddy Sammeta, V., Anderson, B.M., Norris, J.D., Torrice, C.D., Joiner, C., Liu, S., Li, H., Popov, K.I., Fanning, S.W., McDonnell, D.P., Willson, T.M.

(2023) Helv Chim Acta 106

• DOI: https://doi.org/10.1002/hlca.202300097

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 60.19 kDa 
• Atom Count: 4,019 
• Modelled Residue Count: 465 
• 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 E7EWM1 (Homo sapiens) Explore E7EWM1  Go to UniProtKB:  E7EWM1
GTEx:  ENSG00000140396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
61Z (Subject of Investigation/LOI)	E [auth A], F [auth B]	2-(2-chloro-5-phenylthieno[2,3-d]pyrimidin-4-yl)-2,3-dihydro-1H-isoindol-5-ol C20 H14 Cl N3 O S UEFPXXUPWRHSCV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.221 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.094	α = 90
b = 83.456	β = 108.52
c = 58.42	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: 2022-08-03 
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: 2022-08-03
  Type: Initial release
  
• Version 1.1: 2022-08-10
  Changes: Derived calculations
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2024-02-14
  Changes: Database references