5GTR

estrogen receptor alpha in complex with a stabilized peptide antagonist 6

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.367 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.228 

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Literature

Structural Basis of Inhibition of ER alpha-Coactivator Interaction by High-Affinity N-Terminus Isoaspartic Acid Tethered Helical Peptides

Xie, M., Zhao, H., Liu, Q., Zhu, Y., Yin, F., Liang, Y., Jiang, Y., Wang, D., Hu, K., Qin, X., Wang, Z., Wu, Y., Xu, N., Ye, X., Wang, T., Li, Z.

(2017) J Med Chem 60: 8731-8740

  • DOI: 10.1021/acs.jmedchem.7b00732
  • Primary Citation of Related Structures:  
    5GS4, 5GTR

  • PubMed Abstract: 

    • Direct inhibition of the protein-protein interaction of ERα and its endogenous coactivators with a cell permeable stabilized peptide may offer a novel, promising strategy for combating ERα positive breast cancers. Here, we report the co-crystal structure of a helical peptide stabilized by a N-terminal unnatural cross-linked aspartic acid (TD) in complex with the ERα ligand binding domain (LBD) ...

    Direct inhibition of the protein-protein interaction of ERα and its endogenous coactivators with a cell permeable stabilized peptide may offer a novel, promising strategy for combating ERα positive breast cancers. Here, we report the co-crystal structure of a helical peptide stabilized by a N-terminal unnatural cross-linked aspartic acid (TD) in complex with the ERα ligand binding domain (LBD). We designed a series of peptides and peptide 6 that showed direct and high-affinity binding to ERα with selective antiproliferative activity in ERα positive breast cancer cells. The co-crystal structure of the TD-stabilized peptide 6 in complex with ERα LBD further demonstrates that it forms an α helical conformation and directly binds at the coactivator binding site of ERα. Further studies showed that peptide 6 W could potently inhibit cellular ERα's transcriptional activity. This approach demonstrates the potential of TD stabilized peptides to modulate various intracellular protein-protein interactions involved in a range of disorders.

    Organizational Affiliation: 

    School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University , Shenzhen 518055, China.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorA243Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ARG-IAS-ILE-0JY-DPP-ARG-0JY-0JY-GLN-NH2B [auth C]10unidentifiedMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EST
Query on EST
Download Ideal Coordinates CCD File 
C [auth A]ESTRADIOL
C18 H24 O2
VOXZDWNPVJITMN-ZBRFXRBCSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DPP
Query on DPP		B [auth C]L-PEPTIDE LINKINGC3 H8 N2 O2ALA
Binding Affinity Annotations 
IDSourceBinding Affinity
EST BindingDB:  5GTR Ki: min: 0.11, max: 100 (nM) from 13 assay(s)
Kd: min: 0.2, max: 100 (nM) from 4 assay(s)
IC50: min: 1.00e-2, max: 46 (nM) from 46 assay(s)
EC50: min: 4.00e-3, max: 10 (nM) from 52 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.367 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.228 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.787α = 90
b = 60.219β = 90
c = 66.457γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina21102007 and 21372023

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Data collection
  • Version 1.2: 2017-12-20
    Changes: Database references