5KCT

Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with an N-ethyl, 4-chlorobenzyl OBHS-N derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 Physiology and Biophysics, University of Illinois, Chicago, Illinois, USA.,Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, USA.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, State Key Laboratory of Virology, Wuhan University School of Pharmaceutical Sciences, Wuhan, China.,Department of Molecular and Integrative Physiology, University of Illinois, Urbana, Illinois, USA.,Department of Chemistry, University of Illinois, Urbana, Illinois, USA.,Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Estrogen receptor
A, B
257Homo sapiensMutation(s): 1 
Gene Names: ESR1 (ESR, NR3A1)
Find proteins for P03372 (Homo sapiens)
Go to Gene View: ESR1
Go to UniProtKB:  P03372
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NCOA2
C, D
14Homo sapiensMutation(s): 0 
Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OB6
Query on OB6

Download SDF File 
Download CCD File 
B
(1S,2R,4S)-N-(4-chlorophenyl)-N-ethyl-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonamide
C26 H24 Cl N O5 S
NQOVQKVPQWLWNF-PPJWLVRDSA-N
 Ligand Interaction
OB7
Query on OB7

Download SDF File 
Download CCD File 
A
(1R,2S,4R)-N-(4-chlorophenyl)-N-ethyl-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonamide
C26 H24 Cl N O5 S
NQOVQKVPQWLWNF-UMFSSWHCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OB7IC50: 430 nM BINDINGMOAD
OB6IC50: 430 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.872α = 90.00
b = 81.560β = 110.18
c = 58.914γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references
  • Version 1.2: 2016-12-28
    Type: Database references