Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 35.29 kDa 
• Atom Count: 2263 
• Modelled Residue Count: 284 
• Deposited Residue Count: 327 
• Unique protein chains: 1

3HB4

17beta-hydroxysteroid dehydrogenase type1 complexed with E2B

• DOI: 10.2210/pdb3HB4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2009-05-04 Released: 2009-12-15 
• Deposition Author(s): Mazumdar, M., Fournier, D., Zhu, D.-W., Cadot, C., Poirier, D., Lin, S.-X.

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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 

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

• PubMed: 19929851 
• DOI: 10.1042/BJ20091020
• Primary Citation of Related Structures:  
  3HB5, 3HB4


• 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estradiol 17-beta-dehydrogenase 1	X	327	Homo sapiens	Mutation(s): 0  Gene Names: HSD17B1, E17KSR, EDH17B1, EDH17B2, EDHB17, SDR28C1 EC: 1.1.1.62 (PDB Primary Data), 1.1.1.51 (UniProt)
Find proteins for P14061 (Homo sapiens) Explore P14061  Go to UniProtKB:  P14061
NIH Common Fund Data Resources
PHAROS:  P14061 GTEx:  ENSG00000108786

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E2B	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
E2B	Ki :  0.8999999761581421   nM  PDBBind
E2B	IC50:  44   nM  BindingDB
E2B	IC50:  27   nM  BindingDB

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 = 123.08	α = 90
b = 43.7	β = 100.74
c = 60.51	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-04 
• Released Date: 2009-12-15 
Deposition Author(s): Mazumdar, M., Fournier, D., Zhu, D.-W., Cadot, C., Poirier, D., Lin, S.-X.

Revision History  

• 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