5T97 | pdb_00005t97

ESTROGEN RECEPTOR ALPHA LIGAND BINDING DOMAIN IN COMPLEX WITH (2E)-3-(4-{(1R)-6-hydroxy-1-methyl-2-[4-(propan-2 -yl)phenyl]-1,2,3,4- tetrahydroisoquinolin-1-yl}phenyl)prop-2-enoic acid

• PDB DOI: https://doi.org/10.2210/pdb5T97/pdb

• Classification: HORMONE RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-09-09 Released: 2017-03-29 
• Deposition Author(s): Kirby, C.A., Baird, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.291 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Discovery of an Acrylic Acid Based Tetrahydroisoquinoline as an Orally Bioavailable Selective Estrogen Receptor Degrader for ER alpha + Breast Cancer.

Burks, H.E., Abrams, T., Kirby, C.A., Baird, J., Fekete, A., Hamann, L.G., Kim, S., Lombardo, F., Loo, A., Lubicka, D., Macchi, K., McDonnell, D.P., Mishina, Y., Norris, J.D., Nunez, J., Saran, C., Sun, Y., Thomsen, N.M., Wang, C., Wang, J., Peukert, S.

(2017) J Med Chem 60: 2790-2818

• PubMed: 28296398 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b01468
• Primary Citation Related Structures: 
  5T92, 5T97


• PubMed Abstract: 
  

  Tetrahydroisoquinoline 40 has been identified as a potent ERα antagonist and selective estrogen receptor degrader (SERD), exhibiting good oral bioavailability, antitumor efficacy, and SERD activity in vivo. We outline the discovery and chemical optimization of the THIQ scaffold leading to THIQ 40 and showcase the racemization of the scaffold, pharmacokinetic studies in preclinical species, and the in vivo efficacy of THIQ 40 in a MCF-7 human breast cancer xenograft model.

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Organizational Affiliation: 
• Novartis Institutes for BioMedical Research , 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.
Department of Pharmacology and Cancer Biology, Duke University School of Medicine , Durham, North Carolina 27710, United States.

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: 58.65 kDa 
• Atom Count: 3,010 
• Modeled Residue Count: 368 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	254	Homo sapiens	Mutation(s): 0  Gene Names: ESR1, ESR, NR3A1
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
782	C [auth A], D [auth B]	(2E)-3-(4-{(1R)-6-hydroxy-1-methyl-2-[4-(propan-2-yl)phenyl]-1,2,3,4-tetrahydroisoquinolin-1-yl}phenyl)prop-2-enoic acid C28 H29 N O3 HKXVKUOGCLJVEZ-AJVPWASQSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
782	BindingDB:  5T97	IC50: 34 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.291 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.92	α = 90
b = 51.8	β = 113.13
c = 95.17	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Kirby, C.A., Baird, J.

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2017-04-26
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references