1YIN

Human estrogen receptor alpha ligand-binding domain in complex with compound 3F

• PDB DOI:  https://doi.org/10.2210/pdb1YIN/pdb

• Classification: HORMONE/GROWTH FACTOR RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-01-12 Released: 2005-07-26 
• Deposition Author(s): Fitzgerald, P.M., Sharma, N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.296 
• R-Value Observed: 0.179 

Literature

Estrogen receptor ligands. Part 10: Chromanes: old scaffolds for new SERAMs.

Tan, Q., Blizzard, T.A., Morgan, J.D., Birzin, E.T., Chan, W., Yang, Y.T., Pai, L.Y., Hayes, E.C., DaSilva, C.A., Warrier, S., Yudkovitz, J., Wilkinson, H.A., Sharma, N., Fitzgerald, P.M., Li, S., Colwell, L., Fisher, J.E., Adamski, S., Reszka, A.A., Kimmel, D., DiNinno, F., Rohrer, S.P., Freedman, L.P., Schaeffer, J.M., Hammond, M.L.

(2005) Bioorg Med Chem Lett 15: 1675-1681

• PubMed: 15745820 
• DOI: https://doi.org/10.1016/j.bmcl.2005.01.046
• Primary Citation of Related Structures:  
  1YIM, 1YIN


• PubMed Abstract: 
  

The discovery, synthesis, and SAR of chromanes as ER alpha subtype selective ligands are described. X-ray studies revealed that the origin of the ER alpha-selectivity resulted from a C-4 trans methyl substitution to the cis-2,3-diphenyl-chromane platform. Selected compounds from this class demonstrated very potent in vivo antagonism of estradiol in an immature rat uterine weight assay, effectively inhibited ovariectomy-induced bone resorption in a 42 days treatment paradigm, and lowered serum cholesterol levels in ovx'd adult rat models. The best antagonists 8F and 12F also exhibited potent inhibition of MCF-7 cell growth and were shown to be estrogen receptor down-regulators (SERDs).

---

Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 2000, RY800-B107, Rahway, NJ 07065, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.79 kDa 
• Atom Count: 2,026 
• Modelled Residue Count: 241 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A	248	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CM3	B [auth A]	(2R,3R,4S)-5-FLUORO-3-(4-HYDROXYPHENYL)-4-METHYL-2-[4-(2-PIPERIDIN-1-YLETHOXY)PHENYL]CHROMAN-6-OL C29 H32 F N O4 KOYRLVBQHJNLQX-IFVHXUSFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CM3	BindingDB:  1YIN	IC50: 0.8 (nM) from 1 assay(s)
	Binding MOAD:  1YIN	IC50: 1.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.296 
• R-Value Observed: 0.179 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.85	α = 90
b = 58.85	β = 90
c = 277.83	γ = 120

Software Package:

Software Name	Purpose
X-GEN	data scaling
X-GEN	data reduction
SHELXL	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-26 
Deposition Author(s): Fitzgerald, P.M., Sharma, N.

Revision History  

• Version 1.0: 2005-07-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description