3HB4

17beta-hydroxysteroid dehydrogenase type1 complexed with E2B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Binary and ternary crystal structure analyses of a novel inhibitor with 17beta-HSD type 1: a lead compound for breast cancer therapy.

Mazumdar, M.Fournier, D.Zhu, D.W.Cadot, C.Poirier, D.Lin, S.X.

(2009) Biochem J 424: 357-366

  • DOI: https://doi.org/10.1042/BJ20091020
  • Primary Citation of Related Structures:  
    3HB4, 3HB5

  • PubMed Abstract: 

    Oestradiol is a well-characterized sex hormone that stimulates breast cancer and other oestrogen-related diseases. 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD1) catalyses the last step in the synthesis of oestradiol and androstenediol in breast tumour tissue. The enzyme's high expression and activity after simultaneous blockade of oestrogen receptors and inhibition of aromatase in the tumour shows the necessity for its inhibition as a requirement for breast cancer therapy. In the present paper, we report structures of the binary and ternary complexes of 17beta-HSD1 with a new inhibitor E2B {3-[3',17'beta-dihydroxyestra-1',3',5'(10')-trien-16'beta-methyl]benzamide}, and the enzyme inhibition by the later. The IC50 value for E2B was determined to be 42 nM in T47D cells. Multiple interactions between E2B and the enzyme include hydrogen bonds and hydrophobic interactions, as well as pi-pi interactions. A kinetic study demonstrated that E2B inhibits the enzyme's reduction forming oestradiol from oestrone, with a Ki of 0.9+/-0.15 nM. Such strong inhibition is in agreement with its extensive interaction with the enzyme, suggesting its potential as a lead compound for breast cancer therapy. In fact, this possibility is enhanced by its capacity for cell penetration similar to natural steroids. Such inhibitors that block oestrogen synthesis to suppress the sulfatase pathway producing oestradiol can be used in adjuvant therapies with oestrogen receptor blockade, opening a new orientation of breast cancer treatment.


  • Organizational Affiliation

    Laboratory of Molecular Endocrinology and Oncology, CHUL Research Center (Centre Hospitalier de Université Laval, CHUQ) and Laval University, Quebec, Canada, G1V 4G2.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estradiol 17-beta-dehydrogenase 1A [auth X]327Homo sapiensMutation(s): 0 
EC: 1.1.1.62
UniProt & NIH Common Fund Data Resources
Find proteins for P14061 (Homo sapiens)
Explore P14061 
Go to UniProtKB:  P14061
PHAROS:  P14061
GTEx:  ENSG00000108786 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14061
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E2B
Query on E2B

Download Ideal Coordinates CCD File 
B [auth X]3-{[(9beta,14beta,16alpha,17alpha)-3,17-dihydroxyestra-1,3,5(10)-trien-16-yl]methyl}benzamide
C26 H31 N O3
RSVOVHDOLNWYER-RYZVYYIHSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
E2B PDBBind:  3HB4 Ki: 0.9 (nM) from 1 assay(s)
BindingDB:  3HB4 IC50: min: 27, max: 44 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.08α = 90
b = 43.7β = 100.74
c = 60.51γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
REFMACrefinement
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-04-04
    Changes: Data collection
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations