5AAV

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: 1.95 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


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:  
    5AAV, 5AAU, 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-tetrahyd ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ESTROGEN RECEPTORA252Homo sapiensMutation(s): 4 
Gene Names: ESR1ESRNR3A1
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
NIH Common Fund Data Resources
PHAROS  P03372
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ESTROGEN RECEPTORB252Homo sapiensMutation(s): 4 
Gene Names: ESR1ESRNR3A1
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
NIH Common Fund Data Resources
PHAROS  P03372
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GW5
Query on GW5

Download Ideal Coordinates CCD File 
A, B
(2E)-3-{4-[(1E)-1,2-DIPHENYLBUT-1-ENYL]PHENYL}ACRYLIC ACID
C25 H22 O2
HJQQVNIORAQATK-DDJBQNAASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GW5EC50:  390   nM  BindingDB
GW5IC50:  1270   nM  BindingDB
GW5IC50:  3.200000047683716   nM  BindingDB
GW5IC50:  12825   nM  BindingDB
GW5IC50:  3.240000009536743   nM  Binding MOAD
GW5IC50:  39   nM  BindingDB
GW5IC50:  654   nM  BindingDB
GW5IC50:  1288   nM  BindingDB
GW5IC50:  3.200000047683716   nM  BindingDB
GW5IC50:  4000   nM  BindingDB
GW5IC50:  264   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.488α = 90
b = 51.54β = 90.9
c = 83.705γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • 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