5KCW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.905 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.190 

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:  

  • 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: 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OB9
Query on OB9

Download SDF File 
Download CCD File 
A, B
(1S,2R,4S)-5,6-bis(4-hydroxyphenyl)-N-phenyl-N-(2,2,2-trifluoroethyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonamide
C26 H22 F3 N O5 S
IKDGMHLBCBZLCS-SGIRGMQISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OB9IC50: 190 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.905 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.627α = 90.00
b = 81.529β = 110.93
c = 58.976γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

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
  • Version 1.3: 2017-02-22
    Type: Derived calculations