5AAU

Optimization of a novel binding motif to to (E)-3-(3,5-difluoro-4-((1R,3R)-2-(2-fluoro-2-methylpropyl)-3-methyl-2,3,4,9-tetrahydro-1H- pyrido(3,4-b)indol-1-yl)phenyl)acrylic acid (AZD9496), a potent and orally bioavailable selective estrogen receptor downregulator and antagonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Optimization of a Novel Binding Motif to (E)-3-(3,5-Difluoro-4-((1R,3R)-2-(2-Fluoro-2-Methylpropyl)-3-Methyl-2, 3,4,9-Tetrahydro-1H-Pyrido[3,4-B]Indol-1-Yl)Phenyl)Acrylic Acid (Azd9496), a Potent and Orally Bioavailable Selective Estrogen Receptor Downregulator and Antagonist.

De Savi, C.Bradbury, R.H.Rabow, A.A.Norman, R.A.De Almeida, C.Andrews, D.M.Ballard, P.Buttar, D.Callis, R.Currie, G.S.Davies, C.Donald, C.Feron, L.Hayter, B.R.Hussain, S.Karoutchi, G.Lamont, S.Macfaul, P.A.Moss, T.A.Pearson, S.Tonge, M.Walker, G.Weir, H.Wilson, Z.

(2015) J Med Chem 58: 8128

  • DOI: 10.1021/acs.jmedchem.5b00984
  • Primary Citation of Related Structures:  
    5AAU, 5AAV, 5ACC

  • PubMed Abstract: 
  • The discovery of an orally bioavailable selective estrogen receptor downregulator (SERD) with equivalent potency and preclinical pharmacology to the intramuscular SERD fulvestrant is described. A directed screen identified the 1-aryl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole motif as a novel, druglike ER ligand ...

    The discovery of an orally bioavailable selective estrogen receptor downregulator (SERD) with equivalent potency and preclinical pharmacology to the intramuscular SERD fulvestrant is described. A directed screen identified the 1-aryl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole motif as a novel, druglike ER ligand. Aided by crystal structures of novel ligands bound to an ER construct, medicinal chemistry iterations led to (E)-3-(3,5-difluoro-4-((1R,3R)-2-(2-fluoro-2-methylpropyl)-3-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indol-1-yl)phenyl)acrylic acid (30b, AZD9496), a clinical candidate with high oral bioavailability across preclinical species that is currently being evaluated in phase I clinical trials for the treatment of advanced estrogen receptor (ER) positive breast cancer.


    Related Citations: 
    • Azd9496: An Oral Estrogen Receptor Inhibitor that Blocks the Growth of Er-Positive and Esr1-Mutant Breast Tumors in Preclinical Models.
      Weir, H.M., Bradbury, R.H., Lawson, M., Rabow, A.A., Buttar, D., Callis, R.J., Curwen, J.O., De Almeida, C., Ballard, P., Hulse, M., Donald, C.S., Feron, L.J.L., Karoutchi, G., Macfaul, P., Moss, T., Norman, R.A., Pearson, S.E., Tonge, M., Davies, G., Walker, G.E., Wilson, Z., Rowlinson, R., Powell, S., Sadler, C., Richmond, G., Ladd, B., Pazolli, E., Mazzola, A.M., D'Cruz, C., De Savi, C.
      (2016) Cancer Res 76: 3307

    Organizational Affiliation

    Oncology iMed, AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ESTROGEN RECEPTORA, B252Homo sapiensMutation(s): 3 
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
XBR
Query on XBR

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
3-(1-(4-Chlorophenyl)-3,4-dihydro-1H-pyrido(3,4-b)indol-2(9H)-yl)propanoic acid
C20 H19 Cl N2 O2
LVUWGHOKMIGPFO-HXUWFJFHSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
XBR BindingDB:  5AAU IC50: min: 3715, max: 1.38e+4 (nM) from 2 assay(s)
Binding MOAD:  5AAU IC50: 1.38e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.407α = 90
b = 51.396β = 93.66
c = 85.181γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Database references
  • Version 1.2: 2016-10-12
    Changes: Database references