Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
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)

Macromolecule Content

• Total Structure Weight: 62.81 kDa 
• Atom Count: 4042 
• Modelled Residue Count: 495 
• Deposited Residue Count: 542 
• Unique protein chains: 2

2Q6J

Crystal Structure of Estrogen Receptor alpha Complexed to a B-N Substituted Ligand

• PDB DOI: 10.2210/pdb2Q6J/pdb

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


• Deposited: 2007-06-05 Released: 2007-06-26 
• Deposition Author(s): Zhou, H., Nettles, K.W., Bruning, J.B., Kim, Y., Joachimiak, A., Sharma, S., Carlson, K.E., Stossi, F., Katzenellenbogen, B.S., Greene, G.L., Katzenellenbogen, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.297 
• R-Value Work: 0.227 
• R-Value Observed: 0.231 

Literature

Elemental isomerism: a boron-nitrogen surrogate for a carbon-carbon double bond increases the chemical diversity of estrogen receptor ligands

Zhou, H.-B., Nettles, K.W., Bruning, J.B., Kim, Y., Joachimiak, A., Sharma, S., Carlson, K.E., Stossi, F., Katzenellenbogen, B.S., Greene, G.L., Katzenellenbogen, J.A.

(2007) Chem Biol 14: 659-669

• PubMed: 17584613 
• DOI: 10.1016/j.chembiol.2007.04.009
• Primary Citation of Related Structures:  
  2Q6J


• PubMed Abstract: 
  

To increase the chemical diversity of bioactive molecules by incorporating unusual elements, we have examined the replacement of a C=C double bond with the isoelectronic, isostructural B-N bond in the context of nonsteroidal estrogen receptor (ER) ligands. While the B-N bond was hydrolytically labile in the unhindered cyclofenil system, the more hindered anilino dimesitylboranes, analogs of triarylethylene estrogens, were easily prepared, hydrolytically stable, and demonstrated substantial affinity for ERs. X-ray analysis of one ERalpha-ligand complex revealed steric clashes with the para methyl groups distorting the receptor; removal of these groups resulted in an increase in affinity, potency, and transcriptional efficacy. These studies define the structural determinants of stability and cellular bioactivity of a B-N for C=C substitution in nonsteroidal estrogens and provide a framework for further exploration of "elemental isomerism" for diversification of drug-like molecules.

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Organizational Affiliation: 

Department of Chemistry, University of Illinois, Urbana, IL 61801, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	258	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GRIP peptide	C, D	13	Mus musculus	Mutation(s): 0  Gene Names: Ncoa2, Grip1, Src2, Tif2
UniProt & NIH Common Fund Data Resources
Find proteins for Q61026 (Mus musculus) Explore Q61026  Go to UniProtKB:  Q61026
IMPC:  MGI:1276533

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A48	E [auth A], F [auth B]	4-[(DIMESITYLBORYL)(2,2,2-TRIFLUOROETHYL)AMINO]PHENOL C26 H29 B F3 N O DWBQXWOHSLDMOS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.297 
• R-Value Work: 0.227 
• R-Value Observed: 0.231 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.551	α = 90
b = 79.802	β = 109.88
c = 58.328	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-06-05 
• Released Date: 2007-06-26 
Deposition Author(s): Zhou, H., Nettles, K.W., Bruning, J.B., Kim, Y., Joachimiak, A., Sharma, S., Carlson, K.E., Stossi, F., Katzenellenbogen, B.S., Greene, G.L., Katzenellenbogen, J.A.

Revision History  

• Version 1.0: 2007-06-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations