1I5R

TYPE 1 17-BETA HYDROXYSTEROID DEHYDROGENASE EM1745 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A concerted, rational design of type 1 17beta-hydroxysteroid dehydrogenase inhibitors: estradiol-adenosine hybrids with high affinity

Qiu, W.Campbell, R.L.Gangloff, A.Dupuis, P.Boivin, R.P.Tremblay, M.R.Poirier, D.Lin, S.X.

(2002) FASEB J. 16: 1829-1831

  • DOI: 10.1096/fj.02-0026fje

  • PubMed Abstract: 
  • Human estrogenic 17beta-hydroxysteroid dehydrogenase (17beta-HSD type 1) catalyzes the final step in the synthesis of active estrogens that stimulate the proliferation of breast cancer cells. Based on the initial premise to make use of the binding en ...

    Human estrogenic 17beta-hydroxysteroid dehydrogenase (17beta-HSD type 1) catalyzes the final step in the synthesis of active estrogens that stimulate the proliferation of breast cancer cells. Based on the initial premise to make use of the binding energies of both the substrate and cofactor sites, and molecular modeling starting from the enzyme structure, several estradiol-adenosine hybrids were designed and synthesized. Among these hybrids, EM-1745 with a linker of 8-CH2 groups is proved to be the best competitive inhibitor with a Ki of 3.0 +/- 0.8 nM. The crystal structure of the EM-1745 enzyme complex at 1.6 A provides evidence at atomic resolution of strong interactions between both the steroid and cofactor moieties and the enzyme molecule, as illustrated by a deltaA-weighted 2Fo-Fc electron density map contoured at 3.0 delta. The substrate entry loop is further stabilized in this complex compared with previous complexes of the enzyme. These results confirm our initial strategy of combining studies of structural biology and enzyme mechanism in the inhibitor design, which may be applied to other steroidogenic enzymes involved in human diseases.


    Organizational Affiliation

    Oncology and Molecular Endocrinology Research Center, Laval University Medical Center (CHUL) and Laval University, Quebec, G1V 4G2, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYPE 1 17 BETA-HYDROXYSTEROID DEHYDROGENASE
A
327Homo sapiensMutation(s): 0 
Gene Names: HSD17B1 (E17KSR, EDH17B1, EDH17B2, EDHB17, SDR28C1)
EC: 1.1.1.62
Find proteins for P14061 (Homo sapiens)
Go to Gene View: HSD17B1
Go to UniProtKB:  P14061
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HYC
Query on HYC

Download SDF File 
Download CCD File 
A
O5'-[9-(3,17B-DIHYDROXY-1,3,5(10)-ESTRATRIEN-16B-YL)-NONANOYL]ADENOSINE
EM-1745
C37 H51 N5 O7
CKSDYJASHNGOOS-KTXOUVACSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HYCKi: 3 nM (99) BINDINGDB
HYCIC50: 8 - 52 nM (99) BINDINGDB
HYCKi: 3 nM BINDINGMOAD
HYCKi: 3 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 119.272α = 90.00
b = 42.706β = 99.16
c = 58.732γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance