6DFN

Crystal structure of estrogen receptor alpha in complex with receptor degrader 16aa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Unexpected equivalent potency of a constrained chromene enantiomeric pair rationalized by co-crystal structures in complex with estrogen receptor alpha.

Zhang, B.Kiefer, J.R.Blake, R.A.Chang, J.H.Hartman, S.Ingalla, E.R.Kleinheinz, T.Mody, V.Nannini, M.Ortwine, D.F.Ran, Y.Sambrone, A.Sampath, D.Vinogradova, M.Zhong, Y.Nwachukwu, J.C.Nettles, K.W.Lai, T.Liao, J.Zheng, X.Chen, H.Wang, X.Liang, J.

(2019) Bioorg. Med. Chem. Lett. 29: 905-911

  • DOI: 10.1016/j.bmcl.2019.01.036
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Despite tremendous progress made in the understanding of the ERα signaling pathway and the approval of many therapeutic agents, ER+ breast cancer continues to be a leading cause of cancer death in women. We set out to discover compounds with a dual m ...

    Despite tremendous progress made in the understanding of the ERα signaling pathway and the approval of many therapeutic agents, ER+ breast cancer continues to be a leading cause of cancer death in women. We set out to discover compounds with a dual mechanism of action in which they not only compete with estradiol for binding with ERα, but also can induce the degradation of the ERα protein itself. We were attracted to the constrained chromenes containing a tetracyclic benzopyranobenzoxepine scaffold, which were reported as potent selective estrogen receptor modulators (SERMs). Incorporation of a fluoromethyl azetidine side chain yielded highly potent and efficacious selective estrogen receptor degraders (SERDs), such as 16aa and surprisingly, also its enantiomeric pair 16ab. Co-crystal structures of the enantiomeric pair 16aa and 16ab in complex with ERα revealed default (mimics the A-D rings of endogenous ligand estradiol) and core-flipped binding modes, rationalizing the equivalent potency observed for these enantiomers in the ERα degradation and MCF-7 anti-proliferation assays.


    Organizational Affiliation

    Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: liang.jun@gene.com.,WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China.,Department of Integrated Structural and Computational Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.,Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: zhang.birong@gene.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Estrogen receptor
A, B, C, D
280Homo sapiensMutation(s): 0 
Gene Names: ESR1 (ESR, NR3A1)
Find proteins for P03372 (Homo sapiens)
Go to Gene View: ESR1
Go to UniProtKB:  P03372
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G9J
Query on G9J

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Download CCD File 
A, B, C, D
(2S)-3-(3-hydroxyphenyl)-2-(4-iodophenyl)-4-methyl-2H-1-benzopyran-6-ol
C22 H17 I O3
RWKXMXMLZHFKIZ-QFIPXVFZSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
G91
Query on G91

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Download CCD File 
B, D
(8S)-8-(4-{2-[3-(fluoromethyl)azetidin-1-yl]ethoxy}phenyl)-1,8-dihydro-2H-[1]benzopyrano[4,3-d][1]benzoxepine-5,11-diol
C29 H28 F N O5
OXWBLBDJUUJFFV-LJAQVGFWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.247 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 53.089α = 86.05
b = 59.134β = 74.92
c = 94.180γ = 63.34
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-03-06
    Type: Data collection, Database references