4WDW

17beta-HSD5 in complex with 3,6-dihydropyridin-1(2H)-yl(5-methyl-1H-indol-2-yl)methanone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding.

Amano, Y.Yamaguchi, T.Niimi, T.Sakashita, H.

(2015) Acta Crystallogr D Biol Crystallogr 71: 918-927

  • DOI: https://doi.org/10.1107/S1399004715002175
  • Primary Citation of Related Structures:  
    4WDT, 4WDU, 4WDW, 4WDX, 4XVD, 4XVE

  • PubMed Abstract: 

    Type 5 17β-hydroxysteroid dehydrogenase (17β-HSD5) is an aldo-keto reductase expressed in the human prostate which catalyzes the conversion of androstenedione to testosterone. Testosterone is converted to 5α-dihydrotestosterone, which is present at high concentrations in patients with castration-resistant prostate cancer (CRPC). Inhibition of 17β-HSD5 is therefore considered to be a promising therapy for treating CRPC. In the present study, crystal structures of complexes of 17β-HSD5 with structurally diverse inhibitors derived from high-throughput screening were determined. In the structures of the complexes, various functional groups, including amide, nitro, pyrazole and hydroxyl groups, form hydrogen bonds to the catalytic residues His117 and Tyr55. In addition, major conformational changes of 17β-HSD5 were observed following the binding of the structurally diverse inhibitors. These results demonstrate interactions between 17β-HSD5 and inhibitors at the atomic level and enable structure-based drug design for anti-CRPC therapy.


  • Organizational Affiliation

    Drug Discovery Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldo-keto reductase family 1 member C3
A, B
331Homo sapiensMutation(s): 1 
Gene Names: AKR1C3DDH1HSD17B5KIAA0119PGFS
EC: 1.1.1.64 (PDB Primary Data), 1.1.1 (UniProt), 1.1.1.210 (UniProt), 1.1.1.53 (UniProt), 1.1.1.62 (UniProt), 1.1.1.357 (UniProt), 1.1.1.188 (UniProt), 1.1.1.239 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42330 (Homo sapiens)
Explore P42330 
Go to UniProtKB:  P42330
PHAROS:  P42330
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42330
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
WDW BindingDB:  4WDW IC50: 2800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.129α = 81.03
b = 57.917β = 69.72
c = 60.333γ = 79.11
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references
  • Version 1.2: 2017-10-04
    Changes: Data collection, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.3: 2022-12-14
    Changes: Database references, Refinement description