7YMK

Estrogen Receptor Alpha Ligand Binding Domain C381S C417S Y537S Mutant in Complex with an Covalent Selective Estrogen Receptor Degrader 29c and GRIP Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of novel covalent selective estrogen receptor degraders against endocrine-resistant breast cancer.

Wang, Y.Min, J.Deng, X.Feng, T.Hu, H.Guo, X.Cheng, Y.Xie, B.Yang, Y.Chen, C.C.Guo, R.T.Dong, C.Zhou, H.B.

(2023) Acta Pharm Sin B 13: 4963-4982

  • DOI: https://doi.org/10.1016/j.apsb.2023.05.005
  • Primary Citation of Related Structures:  
    7YMK

  • PubMed Abstract: 

    Endocrine-resistance remains a major challenge in estrogen receptor α positive (ER α + ) breast cancer (BC) treatment and constitutively active somatic mutations in ER α are a common mechanism. There is an urgent need to develop novel drugs with new mode of mechanism to fight endocrine-resistance. Given aberrant ER α activity, we herein report the identification of novel covalent selective estrogen receptor degraders (cSERDs) possessing the advantages of both covalent and degradation strategies. A highly potent cSERD 29c was identified with superior anti-proliferative activity than fulvestrant against a panel of ER α + breast cancer cell lines including mutant ER α . Crystal structure of ER α 29c complex alongside intact mass spectrometry revealed that 29c disrupted ER α protein homeostasis through covalent targeting C530 and strong hydrophobic interaction collied on H11, thus enforcing a unique antagonist conformation and driving the ER α degradation. These significant effects of the cSERD on ER α homeostasis, unlike typical ER α degraders that occur directly via long side chains perturbing the morphology of H12, demonstrating a distinct mechanism of action (MoA). In vivo , 29c showed potent antitumor activity in MCF-7 tumor xenograft models and low toxicity. This proof-of-principle study verifies that novel cSERDs offering new opportunities for the development of innovative therapies for endocrine-resistant BC.


  • Organizational Affiliation

    Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptorA,
C [auth B]
260Homo 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
GTEx:  ENSG00000091831 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Grip peptideB [auth C],
D
8Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
UniProt GroupQ15596
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IX0 (Subject of Investigation/LOI)
Query on IX0

Download Ideal Coordinates CCD File 
F [auth B]N-(4-((1S,4S,6R)-3-(4-hydroxyphenyl)-6-(N-(4-hydroxyphenyl)-N-(2,2,2-trifluoroethyl)sulfamoyl)-7-oxabicyclo[2.2.1]hept-2-en-2-yl)phenyl)-3-methylbut-2-enamide
C31 H29 F3 N2 O6 S
XKGLKTUFCHWUAF-LUXHBGHRSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.481α = 90
b = 101.48β = 90
c = 195.807γ = 90
Software Package:
Software NamePurpose
SAINTdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82103994

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-12-20
    Changes: Database references