7QVJ | pdb_00007qvj

ESTROGEN RECEPTOR ALPHA IN COMPLEX WITH COMPOUND 29


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.216 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Discovery of a Potent and Orally Bioavailable Zwitterionic Series of Selective Estrogen Receptor Degrader-Antagonists.

Scott, J.S.Stead, D.Barlaam, B.Breed, J.Carbajo, R.J.Chiarparin, E.Cureton, N.Davey, P.R.J.Fisher, D.I.Gangl, E.T.Grebe, T.Greenwood, R.D.Hande, S.Hatoum-Mokdad, H.Hughes, S.J.Hunt, T.A.Johnson, T.Kavanagh, S.L.Klinowska, T.C.M.Larner, C.J.B.Lawson, M.Lister, A.S.Longmire, D.Marden, S.McGuire, T.M.McMillan, C.McMurray, L.Morrow, C.J.Nissink, J.W.M.Moss, T.A.O'Donovan, D.H.Polanski, R.Stokes, S.Thakur, K.Trueman, D.Truman, C.Tucker, M.J.Wang, H.Whalley, N.Wu, D.Wu, Y.Yang, B.Yang, W.

(2023) J Med Chem 66: 2918-2945

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01964
  • Primary Citation Related Structures: 
    7QVJ, 7QVL

  • PubMed Abstract: 

    Herein, we report the optimization of a meta-substituted series of selective estrogen receptor degrader (SERD) antagonists for the treatment of ER+ breast cancer. Structure-based design together with the use of modeling and NMR to favor the bioactive conformation led to a highly potent series of basic SERDs with promising physicochemical properties. Issues with hERG activity resulted in a strategy of zwitterion formation and ultimately in the identification of 38 . This compound was shown to be a highly potent SERD capable of effectively degrading ERα in both MCF-7 and CAMA-1 cell lines. The low lipophilicity and zwitterionic nature led to a SERD with a clean secondary pharmacology profile and no hERG activity. Favorable physicochemical properties resulted in good oral bioavailability in preclinical species and potent in vivo activity in a mouse xenograft model.


  • Organizational Affiliation
    • Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 58.33 kDa 
  • Atom Count: 3,755 
  • Modeled Residue Count: 477 
  • Deposited Residue Count: 504 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Estrogen receptor
A, B
252Homo sapiensMutation(s): 4 
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H09
(Subject of Investigation/LOI)

Query on H09



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
2,2-bis(fluoranyl)-3-[(1~{R},3~{R})-1-[6-fluoranyl-3-[2-(3-fluoranylpropylamino)ethoxy]-2-methyl-phenyl]-3-methyl-1,3,4,9-tetrahydropyrido[3,4-b]indol-2-yl]propan-1-ol
C27 H33 F4 N3 O2
AJSOGGXGYQZCBL-WGDIFIGCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.216 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.9α = 90
b = 51.79β = 93.86
c = 85.51γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2023-02-01 
  • Deposition Author(s): Breed, J.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-03-08
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description