2AYR | pdb_00002ayr

A SERM Designed for the Treatment of Uterine Leiomyoma with Unique Tissue Specificity for Uterus and Ovaries in Rats

• PDB DOI: https://doi.org/10.2210/pdb2AYR/pdb

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


• Deposited: 2005-09-07 Released: 2005-11-22 
• Deposition Author(s): Hummel, C.W., Geiser, A.G., Bryant, H.U., Cohen, I.R., Dally, R.D., Fong, K.C., Frank, S.A., Hinklin, R., Jones, S.A., Lewis, G., McCann, D.J., Shepherd, T.A., Tian, H., Rudman, D.G., Wallace, O.B., Wang, Y., Dodge, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.263 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

A selective estrogen receptor modulator designed for the treatment of uterine leiomyoma with unique tissue specificity for uterus and ovaries in rats

Hummel, C.W., Geiser, A.G., Bryant, H.U., Cohen, I.R., Dally, R.D., Fong, K.C., Frank, S.A., Hinklin, R., Jones, S.A., Lewis, G., McCann, D.J., Rudman, D.G., Shepherd, T.A., Tian, H., Wallace, O.B., Wang, Y., Dodge, J.A.

(2005) J Med Chem 48: 6772-6775

• PubMed: 16250633 
• DOI: https://doi.org/10.1021/jm050723z
• Primary Citation Related Structures: 
  2AYR


• PubMed Abstract: 
  

  The design of a novel selective estrogen receptor modulator (SERM) for the potential treatment of uterine leiomyoma is described. 16 (LY2066948-HCl) binds with high affinity to estrogen receptors alpha and beta (ERalpha and ERbeta, respectively) and is a potent uterine antagonist with minimal effects on the ovaries as determined by serum biomarkers and histologic evaluation.

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Organizational Affiliation: 
• Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.81 kDa 
• Atom Count: 2,116 
• Modeled Residue Count: 246 
• 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): 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
L4G	B [auth A]	6-(4-METHYLSULFONYL-PHENYL)-5-[4-(2-PIPERIDIN-1-YLETHOXY)PHENOXY]NAPHTHALEN-2-OL C30 H31 N O5 S NJVFOFMHUJJIMB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.263 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.868	α = 90
b = 58.868	β = 90
c = 276.006	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-22 
Deposition Author(s): Hummel, C.W., Geiser, A.G., Bryant, H.U., Cohen, I.R., Dally, R.D., Fong, K.C., Frank, S.A., Hinklin, R., Jones, S.A., Lewis, G., McCann, D.J., Shepherd, T.A., Tian, H., Rudman, D.G., Wallace, O.B., Wang, Y., Dodge, J.A.

Revision History  

• Version 1.0: 2005-11-22
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2020-02-26
  Changes: Derived calculations
• Version 1.5: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.6: 2023-08-23
  Changes: Data collection, Refinement description