6ZOS

Oestrogen receptor ligand binding domain in complex with compound 18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of AZD9833, a Potent and Orally Bioavailable Selective Estrogen Receptor Degrader and Antagonist.

Scott, J.S.Moss, T.A.Balazs, A.Barlaam, B.Breed, J.Carbajo, R.J.Chiarparin, E.Davey, P.R.J.Delpuech, O.Fawell, S.Fisher, D.I.Gagrica, S.Gangl, E.T.Grebe, T.Greenwood, R.D.Hande, S.Hatoum-Mokdad, H.Herlihy, K.Hughes, S.Hunt, T.A.Huynh, H.Janbon, S.L.M.Johnson, T.Kavanagh, S.Klinowska, T.Lawson, M.Lister, A.S.Marden, S.McGinnity, D.F.Morrow, C.J.Nissink, J.W.M.O'Donovan, D.H.Peng, B.Polanski, R.Stead, D.S.Stokes, S.Thakur, K.Throner, S.R.Tucker, M.J.Varnes, J.Wang, H.Wilson, D.M.Wu, D.Wu, Y.Yang, B.Yang, W.

(2020) J Med Chem 63: 14530-14559

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01163
  • Primary Citation of Related Structures:  
    6ZOQ, 6ZOR, 6ZOS

  • PubMed Abstract: 

    Herein we report the optimization of a series of tricyclic indazoles as selective estrogen receptor degraders (SERD) and antagonists for the treatment of ER + breast cancer. Structure based design together with systematic investigation of each region of the molecular architecture led to the identification of N -[1-(3-fluoropropyl)azetidin-3-yl]-6-[(6 S ,8 R )-8-methyl-7-(2,2,2-trifluoroethyl)-6,7,8,9-tetrahydro-3 H -pyrazolo[4,3- f ]isoquinolin-6-yl]pyridin-3-amine ( 28 ). This compound was demonstrated to be a highly potent SERD that showed a pharmacological profile comparable to fulvestrant in its ability to degrade ERα in both MCF-7 and CAMA-1 cell lines. A stringent control of lipophilicity ensured that 28 had favorable physicochemical and preclinical pharmacokinetic properties for oral administration. This, combined with demonstration of potent in vivo activity in mouse xenograft models, resulted in progression of this compound, also known as AZD9833, into clinical trials.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QNK (Subject of Investigation/LOI)
Query on QNK

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
6-[(6~{S},8~{R})-7-[(1-fluoranylcyclopropyl)methyl]-8-methyl-2,6,8,9-tetrahydropyrazolo[4,3-f]isoquinolin-6-yl]-~{N}-[1-(3-fluoranylpropyl)azetidin-3-yl]pyridin-3-amine
C26 H32 F2 N6
PHBYNJGKPFJBPE-NSYGIPOTSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.19α = 90
b = 51.98β = 92.92
c = 85.3γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-01-20 
  • Deposition Author(s): Breed, J.

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description