6PFM

Crystal structure of GDC-0927 bound to estrogen receptor alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of a C-8 hydroxychromene as a potent degrader of estrogen receptor alpha with improved rat oral exposure over GDC-0927.

Labadie, S.S.Li, J.Blake, R.A.Chang, J.H.Goodacre, S.Hartman, S.J.Liang, W.Kiefer, J.R.Kleinheinz, T.Lai, T.Liao, J.Ortwine, D.F.Mody, V.Ray, N.C.Roussel, F.Vinogradova, M.Yeap, S.K.Zhang, B.Zheng, X.Zbieg, J.R.Liang, J.Wang, X.

(2019) Bioorg Med Chem Lett 29: 2090-2093

  • DOI: 10.1016/j.bmcl.2019.07.013
  • Primary Citation of Related Structures:  
    6PET, 6PFM

  • PubMed Abstract: 
  • Phenolic groups are responsible for the high clearance and low oral bioavailability of the estrogen receptor alpha (ERα) clinical candidate GDC-0927. An exhaustive search for a backup molecule with improved pharmacokinetic (PK) properties identified several metabolically stable analogs, although in general at the expense of the desired potency and degradation efficiency ...

    Phenolic groups are responsible for the high clearance and low oral bioavailability of the estrogen receptor alpha (ERα) clinical candidate GDC-0927. An exhaustive search for a backup molecule with improved pharmacokinetic (PK) properties identified several metabolically stable analogs, although in general at the expense of the desired potency and degradation efficiency. C-8 hydroxychromene 30 is the first example of a phenol-containing chromene that not only maintained excellent potency but also exhibited 10-fold higher oral exposure in rats. The improved in vivo clearance in rat was hypothesized to be the result of C-8 hydroxy group being sterically protected from glucuronide conjugation. The excellent potency underscores the possibility of replacing the presumed indispensable phenolic group at C-6 or C-7 of the chromene core. Co-crystal structures were obtained to highlight the change in key interactions and rationalize the retained potency.


    Organizational Affiliation

    Genentech Inc., South San Francisco, CA 94080, USA. Electronic address: wang.xiaojing@gene.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorB [auth A],
A [auth D]
280Homo sapiensMutation(s): 2 
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
OGJ
Query on OGJ

Download Ideal Coordinates CCD File 
C [auth D],
D [auth A]
(2S)-2-(4-{2-[3-(fluoromethyl)azetidin-1-yl]ethoxy}phenyl)-3-(3-hydroxyphenyl)-4-methyl-2H-1-benzopyran-6-ol
C28 H28 F N O4
KJAAPZIFCQQQKX-NDEPHWFRSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
OGJ BindingDB:  6PFM IC50: min: 0.03, max: 0.38 (nM) from 6 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.106α = 90
b = 144.106β = 90
c = 171.064γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-28
    Changes: Data collection, Database references