2Z4B

Estrogen receptor beta ligand-binding domain complexed to a benzopyran ligand

• PDB DOI: https://doi.org/10.2210/pdb2Z4B/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-06-14 Released: 2007-08-07 
• Deposition Author(s): Wang, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.253 
• R-Value Work: 0.232 

Literature

Benzopyrans as selective estrogen receptor beta agonists (SERBAs). Part 3: Synthesis of cyclopentanone and cyclohexanone intermediates for C-ring modification.

Richardson, T.I., Dodge, J.A., Durst, G.L., Pfeifer, L.A., Shah, J., Wang, Y., Durbin, J.D., Krishnan, V., Norman, B.H.

(2007) Bioorg Med Chem Lett 17: 4824-4828

• PubMed: 17614275 
• DOI: https://doi.org/10.1016/j.bmcl.2007.06.052
• Primary Citation of Related Structures:  
  2Q70, 2Z4B


• PubMed Abstract: 
  

  Benzopyrans are selective estrogen receptor (ER) beta agonists (SERBAs), which bind the ER subtypes alpha and beta in opposite orientations. Here we describe the syntheses of cyclopentanone and cyclohexanone intermediates for SAR studies of the C-ring on the benzopyran scaffold. Modification of the C-ring disrupts binding to ERalpha, thus improving ERbeta selectivity up to 100-fold. X-ray cocrystal structures confirm previously observed binding modes.

---

Organizational Affiliation: 

Lilly Research Laboratories, 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,PQS (software)

Macromolecule Content

• Total Structure Weight: 59.09 kDa 
• Atom Count: 3,595 
• Modelled Residue Count: 445 
• Deposited Residue Count: 514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor beta	A, B	257	Homo sapiens	Mutation(s): 0  Gene Names: ESR2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens) Explore Q92731  Go to UniProtKB:  Q92731
PHAROS:  Q92731 GTEx:  ENSG00000140009

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DC8	C [auth A], D [auth B]	(3AS,4R,9BR)-2,2-DIFLUORO-4-(4-HYDROXYPHENYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL C18 H16 F2 O3 QJSMFUTULGSHNQ-ZOBUZTSGSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DC8	Binding MOAD:  2Z4B	Ki: 0.44 (nM) from 1 assay(s)
	BindingDB:  2Z4B	Ki: 0.44 (nM) from 1 assay(s)
	PDBBind:  2Z4B	Ki: 0.44 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.253 
• R-Value Work: 0.232 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.523	α = 90
b = 63.523	β = 90
c = 250.837	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-07 
Deposition Author(s): Wang, Y.

Revision History  

• Version 1.0: 2007-08-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations