5DX3

Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Stapled Peptide SRC2-P3 and Estradiol

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

  • Deposited: 2015-09-23 Released: 2016-07-20 
  • Deposition Author(s): Speltz, T.E., Fanning, S.W., 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/National Center for Complementary and Integrative Health (NIH/NCCIH), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: 10.1002/anie.201510557
  • Primary Citation of Related Structures:  
    5DXB, 5DXE, 5DXG, 5DX3, 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 ...

    "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. twmoore@uic.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorA261Homo 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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorB261Homo 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
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Stapled Peptide SRC2-P3C, D13Homo sapiensMutation(s): 0 
Gene Names: NCOA2BHLHE75SRC2TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EST (Subject of Investigation/LOI)
Query on EST

Download Ideal Coordinates CCD File 
E [auth A], G [auth B]ESTRADIOL
C18 H24 O2
VOXZDWNPVJITMN-ZBRFXRBCSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
5GM
Query on 5GM
C, DL-PEPTIDE LINKINGC8 H17 N O2ILE
MK8
Query on MK8
C, DL-PEPTIDE LINKINGC7 H15 N O2LEU
Binding Affinity Annotations 
IDSourceBinding Affinity
EST BindingDB:  5DX3 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 45 assay(s)
EC50: min: 4.00e-3, max: 10 (nM) from 51 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.162α = 90
b = 85.851β = 109.09
c = 58.764γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



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/National Center for Complementary and Integrative Health (NIH/NCCIH)United StatesT32 AT007533
National Science Foundation (NSF, United States)United StatesMCA06N060

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2020-02-19
    Changes: Derived calculations