5AAU | pdb_00005aau

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

• PDB DOI: https://doi.org/10.2210/pdb5AAU/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-07-28 Released: 2015-10-14 
• Deposition Author(s): Norman, R.A., Bradbury, R.H., de Almeida, C., Andrews, D.M., Ballard, P., Buttar, D., Callis, R.J., Currie, G.S., Curwen, J.O., Davies, C.D., de Savi, C., Donald, C.S., Feron, L.J.L., Glossop, S.C., Hayter, B.R., Karoutchi, G., Lamont, S.G., MacFaul, P., Moss, T., Pearson, S.E., Rabow, A.A., Tonge, M., Walker, G.E., Weir, H.M., Wilson, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.226 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: other

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

• PubMed: 26407012 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b00984
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Oncology iMed, AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K.
Oncology iMed, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.
Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.05 kDa 
• Atom Count: 3,901 
• Modeled Residue Count: 451 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESTROGEN RECEPTOR	A, B	252	Homo sapiens	Mutation(s): 3
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
PHAROS:  P03372 GTEx:  ENSG00000091831

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XBR	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.226 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.407	α = 90
b = 51.396	β = 93.66
c = 85.181	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Norman, R.A., Bradbury, R.H., de Almeida, C., Andrews, D.M., Ballard, P., Buttar, D., Callis, R.J., Currie, G.S., Curwen, J.O., Davies, C.D., de Savi, C., Donald, C.S., Feron, L.J.L., Glossop, S.C., Hayter, B.R., Karoutchi, G., Lamont, S.G., MacFaul, P., Moss, T., Pearson, S.E., Rabow, A.A., Tonge, M., Walker, G.E., Weir, H.M., Wilson, Z.

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
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description