6SQ0

ERa_L536S (L536S/C381S/C471S,C530S) in complex with a bridged tetracyclic indole (compound 8)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Building Bridges in a Series of Estrogen Receptor Degraders: An Application of Metathesis in Medicinal Chemistry.

Scott, J.S.Breed, J.Carbajo, R.J.Davey, P.R.Greenwood, R.Huynh, H.K.Klinowska, T.Morrow, C.J.Moss, T.A.Polanski, R.Nissink, J.W.M.Varnes, J.Yang, B.

(2019) ACS Med Chem Lett 10: 1492-1497

  • DOI: 10.1021/acsmedchemlett.9b00370
  • Primary Citation of Related Structures:  
    6SQ0, 6SUO

  • PubMed Abstract: 
  • Herein we report the use of metathesis to construct a novel tetracyclic core in a series of estrogen receptor degraders. This improved the chemical stability, as assessed using an NMR-MS based assay, and gave a molecule with excellent physicochemical properties and pharmacokinetics in rat ...

    Herein we report the use of metathesis to construct a novel tetracyclic core in a series of estrogen receptor degraders. This improved the chemical stability, as assessed using an NMR-MS based assay, and gave a molecule with excellent physicochemical properties and pharmacokinetics in rat. X-ray crystallography established minimal perturbation of the bridged compounds relative to the unbridged analogues in the receptor binding pocket. Unfortunately, despite retaining excellent binding to ERα, this adversely affected the ability of the compounds to degrade the receptor.


    Organizational Affiliation

    Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorA, B252Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LRQ (Subject of Investigation/LOI)
Query on LRQ

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
Bridged tetracyclic indole
C27 H27 F3 N2 O2
XPULPVUOUDRKNB-SAEWTEAUSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
LRQ Binding MOAD:  6SQ0 IC50: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.11α = 90
b = 51.62β = 90.98
c = 83.69γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2019-09-03 
  • Released Date: 2019-10-30 
  • Deposition Author(s): Breed, J.

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Derived calculations