5KCC

Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with Oxabicyclic Heptene Sulfonamide (OBHS-N)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Full antagonism of the estrogen receptor without a prototypical ligand side chain.

Srinivasan, S.Nwachukwu, J.C.Bruno, N.E.Dharmarajan, V.Goswami, D.Kastrati, I.Novick, S.Nowak, J.Cavett, V.Zhou, H.B.Boonmuen, N.Zhao, Y.Min, J.Frasor, J.Katzenellenbogen, B.S.Griffin, P.R.Katzenellenbogen, J.A.Nettles, K.W.

(2017) Nat Chem Biol 13: 111-118

  • DOI: 10.1038/nchembio.2236
  • Primary Citation of Related Structures:  
    5KCF, 5KCE, 5KCD, 5KCC, 5KCU, 5KD9, 5KCW, 5KCT

  • PubMed Abstract: 
  • Resistance to endocrine therapies remains a major clinical problem for the treatment of estrogen receptor-α (ERα)-positive breast cancer. On-target side effects limit therapeutic compliance and use for chemoprevention, highlighting an unmet need for ...

    Resistance to endocrine therapies remains a major clinical problem for the treatment of estrogen receptor-α (ERα)-positive breast cancer. On-target side effects limit therapeutic compliance and use for chemoprevention, highlighting an unmet need for new therapies. Here we present a full-antagonist ligand series lacking the prototypical ligand side chain that has been universally used to engender antagonism of ERα through poorly understood structural mechanisms. A series of crystal structures and phenotypic assays reveal a structure-based design strategy with separate design elements for antagonism and degradation of the receptor, and access to a structurally distinct space for further improvements in ligand design. Understanding structural rules that guide ligands to produce diverse ERα-mediated phenotypes has broad implications for the treatment of breast cancer and other estrogen-sensitive aspects of human health including bone homeostasis, energy metabolism, and autoimmunity.


    Organizational Affiliation

    Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorAB257Homo sapiensMutation(s): 1 
Gene Names: ESR1ESRNR3A1
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
NIH Common Fund Data Resources
PHAROS  P03372
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NCOA2CD14Homo sapiensMutation(s): 0 
Gene Names: NCOA2BHLHE75SRC2TIF2
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS  Q15596
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OB1
Query on OB1

Download Ideal Coordinates CCD File 
A, B
(1S,2R,4S)-5,6-bis(4-hydroxyphenyl)-N-phenyl-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonamide
C24 H21 N O5 S
HRIRAPQMJVLREA-YZUZCNPQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.53α = 90
b = 81.16β = 110.8
c = 58.68γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references
  • Version 1.2: 2016-12-28
    Changes: Database references
  • Version 1.3: 2020-02-26
    Changes: Derived calculations