5O6X

17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex with a non-steroidal quinoline based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-based design and profiling of novel 17 beta-HSD14 inhibitors.

Braun, F.Bertoletti, N.Moller, G.Adamski, J.Frotscher, M.Guragossian, N.Madeira Girio, P.A.Le Borgne, M.Ettouati, L.Falson, P.Muller, S.Vollmer, G.Heine, A.Klebe, G.Marchais-Oberwinkler, S.

(2018) Eur J Med Chem 155: 61-76

  • DOI: https://doi.org/10.1016/j.ejmech.2018.05.029
  • Primary Citation of Related Structures:  
    5O42, 5O43, 5O6O, 5O6X, 5O6Z, 5O72, 5O7C

  • PubMed Abstract: 

    The human enzyme 17β-hydroxysteroid dehydrogenase 14 (17β-HSD14) oxidizes the hydroxyl group at position 17 of estradiol and 5-androstenediol using NAD + as cofactor. However, the physiological role of the enzyme remains unclear. We recently described the first class of nonsteroidal inhibitors for this enzyme with compound 1 showing a high 17β-HSD14 inhibitory activity. Its crystal structure was used as starting point for a structure-based optimization in this study. The goal was to develop a promising chemical probe to further investigate the enzyme. The newly designed compounds revealed mostly very high inhibition of the enzyme and for seven of them the crystal structures of the corresponding inhibitor-enzyme complexes were resolved. The crystal structures disclosed that a small change in the substitution pattern of the compounds resulted in an alternative binding mode for one inhibitor. The profiling of a set of the most potent inhibitors identified 13 (K i  = 9 nM) with a good selectivity profile toward three 17β-HSDs and the estrogen receptor alpha. This inhibitor displayed no cytotoxicity, good solubility, and auspicious predicted bioavailability. Overall, 13 is a highly interesting 17β-HSD14 inhibitor, which might be used as chemical probe for further investigation of the target enzyme.


  • Organizational Affiliation

    Institute for Pharmaceutical Chemistry, Philipps University Marburg, 35032, Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
17-beta-hydroxysteroid dehydrogenase 14274Homo sapiensMutation(s): 0 
Gene Names: HSD17B14DHRS10SDR3SDR47C1UNQ502/PRO474
EC: 1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BPX1 (Homo sapiens)
Explore Q9BPX1 
Go to UniProtKB:  Q9BPX1
PHAROS:  Q9BPX1
GTEx:  ENSG00000087076 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BPX1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
9MK Binding MOAD:  5O6X Ki: 6 (nM) from 1 assay(s)
BindingDB:  5O6X Ki: 6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.132α = 90
b = 91.132β = 90
c = 133.345γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyMA-5287/1-1
German Research FoundationGermanyKL-1204/15-1

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-13
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary