1XP6

HUMAN ESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN IN COMPLEX WITH COMPOUND 16

• PDB DOI: https://doi.org/10.2210/pdb1XP6/pdb

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


• Deposited: 2004-10-08 Released: 2004-12-07 
• Deposition Author(s): Fitzgerald, P.M.D., Sharma, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.267 
• R-Value Observed: 0.177 

Literature

Estrogen receptor ligands. Part 9: Dihydrobenzoxathiin SERAMs with alkyl substituted pyrrolidine side chains and linkers.

Blizzard, T.A., Dininno, F., Morgan, J.D., Chen, H.Y., Wu, J.Y., Kim, S., Chan, W., Birzin, E.T., Yang, Y.T., Pai, L.Y., Fitzgerald, P.M., Sharma, N., Li, Y., Zhang, Z., Hayes, E.C., Dasilva, C.A., Tang, W., Rohrer, S.P., Schaeffer, J.M., Hammond, M.L.

(2005) Bioorg Med Chem Lett 15: 107-113

• PubMed: 15582421 
• DOI: https://doi.org/10.1016/j.bmcl.2004.10.036
• Primary Citation of Related Structures:  
  1XP1, 1XP6, 1XP9, 1XPC


• PubMed Abstract: 
  

  A series of dihydrobenzoxathiin SERAMs with alkylated pyrrolidine side chains or alkylated linkers was prepared. Minor modifications in the side chain or linker resulted in significant effects on biological activity, especially in uterine tissue.

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Organizational Affiliation: 

Merck Research Laboratories, RY800-B116, PO Box 2000, Rahway, NJ 07065, 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: 28.79 kDa 
• Atom Count: 2,142 
• Modelled Residue Count: 245 
• 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, NR3A1, ESR
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
AIU	B [auth A]	(2S,3R)-2-(4-{2-[(3S,4S)-3,4-DIMETHYLPYRROLIDIN-1-YL]ETHOXY}PHENYL)-3-(4-HYDROXYPHENYL)-2,3-DIHYDRO-1,4-BENZOXATHIIN-6-OL C28 H31 N O4 S COJFASLRENZFLP-FNZLKOBSSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AIU	PDBBind:  1XP6	IC50: 0.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.267 
• R-Value Observed: 0.177 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.57	α = 90
b = 58.57	β = 90
c = 276.31	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: 2004-12-07 
Deposition Author(s): Fitzgerald, P.M.D., Sharma, N.

Revision History  

• Version 1.0: 2004-12-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations