2QE4

Estrogen receptor alpha ligand-binding domain in complex with a benzopyran agonist

• PDB DOI: https://doi.org/10.2210/pdb2QE4/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-06-22 Released: 2007-09-04 
• Deposition Author(s): Norman, B.H., Richardson, T.I., Dodge, J.A., Pfeifer, L.A., Durst, G.L., Wang, Y., Durbin, J.D., Krishnan, V., Dinn, S.R., Liu, S.Q., Reilly, J.E., Ryter, K.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.279 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 

Literature

Benzopyrans as selective estrogen receptor beta agonists (SERBAs). Part 4: Functionalization of the benzopyran A-ring.

Norman, B.H., Richardson, T.I., Dodge, J.A., Pfeifer, L.A., Durst, G.L., Wang, Y., Durbin, J.D., Krishnan, V., Dinn, S.R., Liu, S., Reilly, J.E., Ryter, K.T.

(2007) Bioorg Med Chem Lett 17: 5082-5085

• PubMed: 17662603 
• DOI: https://doi.org/10.1016/j.bmcl.2007.07.009
• Primary Citation of Related Structures:  
  2JJ3, 2QE4


• PubMed Abstract: 
  

  Benzopyrans are selective estrogen receptor (ER) beta agonists (SERBAs), which bind the ER receptor subtypes alpha and beta in opposite orientations. We have used structure based drug design to show that this unique phenomena can be exploited via substitution at the 8-position of the benzopyran A-ring to disrupt binding to ERalpha, thus improving ERbeta subtype selectivity. X-ray cocrystal structures with ERalpha and ERbeta are supportive of this approach to improve selectivity in this structural class.

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Organizational Affiliation: 

Discovery Chemistry Research, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA. [e-mail]

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: 57.25 kDa 
• Atom Count: 3,353 
• Modelled Residue Count: 411 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	248	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 GTEx:  ENSG00000091831

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JJ3	C [auth A], D [auth B]	(3AS,4R,9BR)-4-(4-HYDROXYPHENYL)-6-(METHOXYMETHYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL C20 H22 O4 RHQLNMNKTIOREN-AOIWGVFYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
JJ3	PDBBind:  2QE4	Ki: 11 (nM) from 1 assay(s)
	BindingDB:  2QE4	Ki: min: 11, max: 11.9 (nM) from 2 assay(s)
	Binding MOAD:  2QE4	Ki: 11 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.279 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.915	α = 90
b = 54.091	β = 91.24
c = 84.169	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-04 
Deposition Author(s): Norman, B.H., Richardson, T.I., Dodge, J.A., Pfeifer, L.A., Durst, G.L., Wang, Y., Durbin, J.D., Krishnan, V., Dinn, S.R., Liu, S.Q., Reilly, J.E., Ryter, K.T.

Revision History  

• Version 1.0: 2007-09-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references
• Version 1.3: 2024-02-21
  Changes: Data collection