RCSB PDB - 5DXB: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Stapled Peptide SRC2-P1 and Estradiol

 5DXB

Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Stapled Peptide SRC2-P1 and Estradiol

  • Classification: Hormone receptor/peptide
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2015-09-23 Released: 2016-07-27 
  • Deposition Author(s): Fanning, S.W., Speltz, T.E., Mayne, C.G., Tajkhorshid, E., Greene, G.L., Moore, T.W.
  • Funding Organization(s): American Association of Colleges of Pharmacy, University of Illinois Cancer Center, Chicago Biomedical Consortium, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director, National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ESTClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Stapled Peptides with gamma-Methylated Hydrocarbon Chains for the Estrogen Receptor/Coactivator Interaction.

Speltz, T.E.Fanning, S.W.Mayne, C.G.Fowler, C.Tajkhorshid, E.Greene, G.L.Moore, T.W.

(2016) Angew Chem Int Ed Engl 55: 4252-4255

  • DOI: https://doi.org/10.1002/anie.201510557
  • Primary Citation of Related Structures:  
    5DX3, 5DXB, 5DXE, 5DXG, 5HYR

  • PubMed Abstract: 

    "Stapled" peptides are typically designed to replace two non-interacting residues with a constraining, olefinic staple. To mimic interacting leucine and isoleucine residues, we have created new amino acids that incorporate a methyl group in the γ-position of the stapling amino acid S5. We have incorporated them into a sequence derived from steroid receptor coactivator 2, which interacts with estrogen receptor α. The best peptide (IC50 =89 nm) replaces isoleucine 689 with an S-γ-methyl stapled amino acid, and has significantly higher affinity than unsubstituted peptides (390 and 760 nm). Through X-ray crystallography and molecular dynamics studies, we show that the conformation taken up by the S-γ-methyl peptide minimizes the syn-pentane interactions between the α- and γ-methyl groups.


  • Organizational Affiliation

    Department of Medicinal Chemistry and Pharmacognosy and UI Cancer Center, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL, 60612, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor261Homo sapiensMutation(s): 1 
Gene Names: ESR1ESRNR3A1
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
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor261Homo sapiensMutation(s): 1 
Gene Names: ESR1ESRNR3A1
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
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2C [auth D],
D [auth E]
13Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
SCH
Query on SCH
A
L-PEPTIDE LINKINGC4 H9 N O2 S2CYS
66D
Query on 66D
C [auth D],
D [auth E]
L-PEPTIDE LINKINGC8 H17 N O2ILE
MK8
Query on MK8
C [auth D],
D [auth E]
L-PEPTIDE LINKINGC7 H15 N O2LEU
Binding Affinity Annotations 
IDSourceBinding Affinity
EST BindingDB:  5DXB Ki: min: 0.11, max: 100 (nM) from 14 assay(s)
Kd: min: 0.2, max: 3.5 (nM) from 3 assay(s)
IC50: min: 1.00e-2, max: 46 (nM) from 50 assay(s)
EC50: min: 4.00e-3, max: 10 (nM) from 53 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.013α = 90
b = 85.939β = 108.41
c = 58.272γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ESTClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Association of Colleges of PharmacyUnited States--
University of Illinois Cancer CenterUnited States--
Chicago Biomedical ConsortiumUnited States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41-GM104601
National Institutes of Health/Office of the DirectorUnited StatesT32-AT007533
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)United States--
National Science Foundation (NSF, United States)United StatesMCA06N060

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2020-02-19
    Changes: Derived calculations