5EN4

Complex of 17-beta-hydroxysteroid dehydrogenase type 14 with inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.129 
  • R-Value Work: 0.108 
  • R-Value Observed: 0.109 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

First Structure-Activity Relationship of 17 beta-Hydroxysteroid Dehydrogenase Type 14 Nonsteroidal Inhibitors and Crystal Structures in Complex with the Enzyme.

Braun, F.Bertoletti, N.Moller, G.Adamski, J.Steinmetzer, T.Salah, M.Abdelsamie, A.S.van Koppen, C.J.Heine, A.Klebe, G.Marchais-Oberwinkler, S.

(2016) J Med Chem 59: 10719-10737

  • DOI: 10.1021/acs.jmedchem.6b01436
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 17β-HSD14 belongs to the SDR family and oxidizes the hydroxyl group at position 17 of estradiol and 5-androstenediol using NAD + as cofactor. The goal of this study was to identify and optimize 17β-HSD14 nonsteroidal inhibitors as well as ...

    17β-HSD14 belongs to the SDR family and oxidizes the hydroxyl group at position 17 of estradiol and 5-androstenediol using NAD + as cofactor. The goal of this study was to identify and optimize 17β-HSD14 nonsteroidal inhibitors as well as to disclose their structure-activity relationship. In a first screen, a library of 17β-HSD1 and 17β-HSD2 inhibitors, selected with respect to scaffold diversity, was tested for 17β-HSD14 inhibition. The most interesting hit was taken as starting point for chemical modification applying a ligand-based approach. The designed compounds were synthesized and tested for 17β-HSD14 inhibitory activity. The two best inhibitors identified in this study have a very high affinity to the enzyme with a K i equal to 7 nM. The strong affinity of these inhibitors to the enzyme active site could be explained by crystallographic structure analysis, which highlighted the role of an extended H-bonding network in the stabilization process. The selectivity of the most potent compounds with respect to 17β-HSD1 and 17β-HSD2 is also addressed.


    Organizational Affiliation

    Institute for Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
17-beta-hydroxysteroid dehydrogenase 14A270Homo sapiensMutation(s): 0 
Gene Names: HSD17B14DHRS10SDR3SDR47C1UNQ502/PRO474
EC: 1.1.1
Find proteins for Q9BPX1 (Homo sapiens)
Explore Q9BPX1 
Go to UniProtKB:  Q9BPX1
NIH Common Fund Data Resources
PHAROS  Q9BPX1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
5Q6
Query on 5Q6

Download CCD File 
A
[2,3-bis(oxidanyl)phenyl]-[6-(2-fluoranyl-3-oxidanyl-phenyl)pyridin-2-yl]methanone
C18 H12 F N O4
OESDFRIOBRBPRO-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5Q6Ki:  64   nM  Binding MOAD
5Q6Ki:  64   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.129 
  • R-Value Work: 0.108 
  • R-Value Observed: 0.109 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.724α = 90
b = 91.724β = 90
c = 135.022γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyKL1204/15-1

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Data collection