4HMN

Crystal structure of human 17beta-hydroxysteroid dehydrogenase type 5 in complex with (4-(4-Chlorophenyl)piperazin-1-yl)(morpholino)methanone (24)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Morpholylureas are a new class of potent and selective inhibitors of the type 5 17-beta-hydroxysteroid dehydrogenase (AKR1C3).

Flanagan, J.U.Atwell, G.J.Heinrich, D.M.Brooke, D.G.Silva, S.Rigoreau, L.J.Trivier, E.Turnbull, A.P.Raynham, T.Jamieson, S.M.Denny, W.A.

(2014) Bioorg Med Chem 22: 967-977

  • DOI: 10.1016/j.bmc.2013.12.050
  • Primary Citation of Related Structures:  
    4HMN

  • PubMed Abstract: 
  • Inhibitors of the aldo-keto reductase enzyme AKR1C3 are of interest as potential drugs for leukemia and hormone-related cancers. A series of non-carboxylate morpholino(phenylpiperazin-1-yl)methanones were prepared by palladium-catalysed coupling of s ...

    Inhibitors of the aldo-keto reductase enzyme AKR1C3 are of interest as potential drugs for leukemia and hormone-related cancers. A series of non-carboxylate morpholino(phenylpiperazin-1-yl)methanones were prepared by palladium-catalysed coupling of substituted phenyl or pyridyl bromides with the known morpholino(piperazin-1-yl)methanone, and shown to be potent (IC50∼100nM) and very isoform-selective inhibitors of AKR1C3. Lipophilic electron-withdrawing substituents on the phenyl ring were positive for activity, as was an H-bond acceptor on the other terminal ring, and the ketone moiety (as a urea) was essential. These structure-activity relationships are consistent with an X-ray structure of a representative compound bound in the AKR1C3 active site, which showed H-bonding between the carbonyl oxygen of the drug and Tyr55 and His117 in the 'oxyanion hole' of the enzyme, with the piperazine bridging unit providing the correct twist to allow the terminal benzene ring to occupy the lipophilic pocket and align with Phe311.


    Organizational Affiliation

    Auckland Cancer Society Research Centre, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand. Electronic address: b.denny@auckland.ac.nz.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aldo-keto reductase family 1 member C3A331Homo sapiensMutation(s): 0 
Gene Names: AKR1C3DDH1HSD17B5KIAA0119PGFS
EC: 1 (PDB Primary Data), 1.1.1.213 (PDB Primary Data), 1.1.1.112 (PDB Primary Data), 1.1.1.188 (PDB Primary Data), 1.1.1.63 (PDB Primary Data), 1.1.1.64 (PDB Primary Data), 1.3.1.20 (PDB Primary Data), 1.1.1.357 (UniProt), 1.1.1.239 (UniProt)
Find proteins for P42330 (Homo sapiens)
Explore P42330 
Go to UniProtKB:  P42330
NIH Common Fund Data Resources
PHAROS  P42330
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
16J
Query on 16J

Download CCD File 
A
[4-(4-chlorophenyl)piperazin-1-yl](morpholin-4-yl)methanone
C15 H20 Cl N3 O2
KDSIRFZJOTZBPT-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
16JIC50:  18   nM  BindingDB
16JIC50:  30000   nM  BindingDB
16JIC50:  110   nM  Binding MOAD
16JIC50:  110   nM  BindingDB
16JIC50:  30000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.956α = 90
b = 64.068β = 90
c = 96.404γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2014-02-26
    Changes: Database references