3DT3 | pdb_00003dt3

Human Estrogen receptor alpha LBD with GW368

• PDB DOI: https://doi.org/10.2210/pdb3DT3/pdb

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


• Deposited: 2008-07-14 Released: 2008-09-09 
• Deposition Author(s): Williams, S.P., Miller, A.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.262 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.203 (Depositor) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Synthesis of 3-alkyl naphthalenes as novel estrogen receptor ligands.

Fang, J., Akwabi-Ameyaw, A., Britton, J.E., Katamreddy, S.R., Navas, F., Miller, A.B., Williams, S.P., Gray, D.W., Orband-Miller, L.A., Shearin, J., Heyer, D.

(2008) Bioorg Med Chem Lett 18: 5075-5077

• PubMed: 18722117 
• DOI: https://doi.org/10.1016/j.bmcl.2008.07.121
• Primary Citation Related Structures: 
  3DT3


• PubMed Abstract: 
  

  A series of estrogen receptor ligands based on a 3-alkyl naphthalene scaffold was synthesized using an intramolecular enolate-alkyne cycloaromatization as the key step. Several of these compounds bearing a C6-OH group were shown to be high affinity ligands. All compounds had similar ERalpha and ERbeta binding affinity ranging from micromolar to low nanomolar.

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Organizational Affiliation: 
• GlaxoSmithKline Research, 5 Moore Drive, Research Triangle Park, NC 27709, 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.

Macromolecule Content 

• Total Structure Weight: 58.96 kDa 
• Atom Count: 3,863 
• Modeled Residue Count: 476 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	255	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 GTEx:  ENSG00000091831

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
369	C [auth A], D [auth B]	5-(4-hydroxyphenoxy)-6-(3-hydroxyphenyl)-7-methylnaphthalen-2-ol C23 H18 O4 OKUBOIRIRQHVSM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.262 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.203 (Depositor) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.309	α = 90
b = 57.996	β = 105.15
c = 88.331	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-09 
Deposition Author(s): Williams, S.P., Miller, A.B.

Revision History  

• Version 1.0: 2008-09-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-03-13
  Changes: Source and taxonomy, Structure summary
• Version 1.5: 2024-04-03
  Changes: Refinement description