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

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

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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: https://doi.org/10.1016/j.bmcl.2019.01.036
  • Primary Citation of Related Structures:  
    6DF6, 6DFN

  • 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 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: zhang.birong@gene.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptor
A, B, C, D
280Homo sapiensMutation(s): 0 
Gene Names: ESR1ESRNR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
PHAROS:  P03372
GTEx:  ENSG00000091831 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on G91

Download Ideal Coordinates CCD File 
G [auth B],
M [auth D]
C29 H28 F N O5
Query on G9J

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E [auth A],
H [auth B],
K [auth C],
L [auth D]
C22 H17 I O3
Query on GOL

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I [auth B],
J [auth B],
N [auth D]
C3 H8 O3
Query on NI

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
G91 Binding MOAD:  6DFN IC50: 55 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.089α = 86.05
b = 59.134β = 74.92
c = 94.18γ = 63.34
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-04-03
    Changes: Refinement description