Crystal structure of GDC-0927 bound to estrogen receptor alpha

Experimental Data Snapshot

  • Resolution: 2.84 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptorA [auth D],
B [auth A]
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
GTEx:  ENSG00000091831 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on OGJ

Download Ideal Coordinates CCD File 
C [auth D],
D [auth A]
C28 H28 F N O4
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

  • 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
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: 2019-07-17
    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
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Refinement description