2NV7

Crystal Structure of Estrogen Receptor Beta Complexed with WAY-555

• PDB DOI: https://doi.org/10.2210/pdb2NV7/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-11-10 Released: 2007-08-21 
• Deposition Author(s): Mewshaw, R.E., Bowen, M.S., Harris, H.A., Xu, Z.B., Manas, E.S., Cohn, S.T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.265 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 

Starting Model: experimental

Literature

ERbeta ligands. Part 5: synthesis and structure-activity relationships of a series of 4'-hydroxyphenyl-aryl-carbaldehyde oxime derivatives.

Mewshaw, R.E., Bowen, S.M., Harris, H.A., Xu, Z.B., Manas, E.S., Cohn, S.T.

(2007) Bioorg Med Chem Lett 17: 902-906

• PubMed: 17188490 
• DOI: https://doi.org/10.1016/j.bmcl.2006.11.066
• Primary Citation of Related Structures:  
  2NV7


• PubMed Abstract: 
  

  A series of 4'-hydroxyphenyl-aryl-carbaldehyde oximes (5b) was prepared and found to have high affinity (4nM) and modest selectivity (39-fold) for estrogen receptor-beta (ERbeta). Substitution of one of the core rings of the scaffold based around these novel ligands further expanded our knowledge in the quest toward achieving high affinity and selectivity for ERbeta. An X-ray co-crystal of structure 11 revealed that the oxime moiety was mimicking the C-ring of genistein, as previously predicted by SAR and docking studies.

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Organizational Affiliation: 

Chemical and Screening Sciences, Wyeth Research, 500 Arcola Road, Collegeville, PA 19426, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 56.68 kDa 
• Atom Count: 4,017 
• Modelled Residue Count: 473 
• Deposited Residue Count: 496 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor beta	A, B	238	Homo sapiens	Mutation(s): 0  Gene Names: ESR2, ESTRB, NR3A2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens) Explore Q92731  Go to UniProtKB:  Q92731
PHAROS:  Q92731 GTEx:  ENSG00000140009

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	C, D	10	N/A	Mutation(s): 0  EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
555	E [auth A], F [auth B]	4-(4-HYDROXYPHENYL)-1-NAPHTHALDEHYDE OXIME C17 H13 N O2 VYQQTWUZKPWPRL-WOJGMQOQSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
555	PDBBind:  2NV7	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.265 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.13	α = 90
b = 88.676	β = 90
c = 100.459	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-21 
Deposition Author(s): Mewshaw, R.E., Bowen, M.S., Harris, H.A., Xu, Z.B., Manas, E.S., Cohn, S.T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-08-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-04-03
  Changes: Refinement description