6K3N

Crystal structure of human estrogen-related receptor gamma ligand binding domain complex with BPA-monoF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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Ligand Structure Quality Assessment 


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Literature

Evaluation of the Influence of Halogenation on the Binding of Bisphenol A to the Estrogen-Related Receptor gamma.

Suyama, K.Kaneko, S.Kesamaru, H.Liu, X.Matsushima, A.Kakuta, Y.Okubo, T.Kasatani, K.Nose, T.

(2020) Chem Res Toxicol 33: 889-902

  • DOI: 10.1021/acs.chemrestox.9b00379
  • Primary Citation of Related Structures:  
    6K3N

  • PubMed Abstract: 
  • Halogenation of organic compounds is one the most important transformations in chemical synthesis and is used for the production of various industrial products. A variety of halogenated bisphenol analogs have recently been developed and are used as alternatives to bisphenol A (BPA), which is a raw material of polycarbonate that has adverse effects in animals ...

    Halogenation of organic compounds is one the most important transformations in chemical synthesis and is used for the production of various industrial products. A variety of halogenated bisphenol analogs have recently been developed and are used as alternatives to bisphenol A (BPA), which is a raw material of polycarbonate that has adverse effects in animals. However, limited information is available on the potential toxicity of the halogenated BPA analogs. In the present study, to assess the latent toxicity of halogenated BPA analogs, we evaluated the binding and transcriptional activities of halogenated BPA analogs to the estrogen-related receptor γ (ERRγ), a nuclear receptor that contributes to the growth of nerves and sexual glands. Fluorinated BPA analogs demonstrated strong ERRγ binding potency, and inverse antagonistic activity, similar to BPA. X-ray crystallography and fragment molecular orbital (FMO) calculation revealed that a fluorine-substituted BPA analog could interact with several amino acid residues of ERRγ-LBD, strengthening the binding affinity of the analogs. The ERRγ binding affinity and transcriptional activity of the halogenated BPAs decreased with the increase in the size and number of halogen atom(s). The IC 50 values, determined by the competitive binding assay, correlated well with the binding energy obtained from the docking calculation, suggesting that the docking calculation could correctly estimate the ERRγ binding potency of the BPA analogs. These results confirmed that ERRγ has a ligand binding pocket that fits very well to BPA. Furthermore, this study showed that the binding affinity of the BPA analogs can be predicted by the docking calculation, indicating the importance of the calculation method in the risk assessment of halogenated compounds.


    Organizational Affiliation

    Department of Chemistry, Faculty and Graduate School of Science, Fukuoka 819-0395, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen-related receptor gammaA227Homo sapiensMutation(s): 0 
Gene Names: ESRRGERR3ERRG2KIAA0832NR3B3
UniProt & NIH Common Fund Data Resources
Find proteins for P62508 (Homo sapiens)
Explore P62508 
Go to UniProtKB:  P62508
PHAROS:  P62508
GTEx:  ENSG00000196482 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62508
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CW6 (Subject of Investigation/LOI)
Query on CW6

Download Ideal Coordinates CCD File 
B [auth A]2-fluoranyl-4-[2-(4-hydroxyphenyl)propan-2-yl]phenol
C15 H15 F O2
XMEGCBLYVCFWLJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CW6 Binding MOAD:  6K3N IC50: 5.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.666α = 90
b = 63.666β = 90
c = 132.212γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release