6FOZ

The crystal structure of P.fluorescens Kynurenine 3-monooxygenase (KMO) in complex with competitive inhibitor No. 13

  • Classification: OXIDOREDUCTASE
  • Organism(s): Pseudomonas fluorescens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-02-08 Released: 2019-08-21 
  • Deposition Author(s): Levy, C.W., Leys, D.
  • Funding Organization(s): Biotechnology and Biological Sciences Research Council, Engineering and Physical Sciences Research Council, Medical Research Council (United Kingdom)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


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Literature

A brain-permeable inhibitor of the neurodegenerative disease target kynurenine 3-monooxygenase prevents accumulation of neurotoxic metabolites.

Zhang, S., Sakuma, M., Deora, G.S., Levy, C.W., Klausing, A., Breda, C., Read, K.D., Edlin, C.D., Ross, B.P., Wright Muelas, M., Day, P.J., O'Hagan, S., Kell, D.B., Schwarcz, R., Leys, D., Heyes, D.J., Giorgini, F., Scrutton, N.S.

(2019) Commun Biol 2: 271-271

  • DOI: https://doi.org/10.1038/s42003-019-0520-5
  • Primary Citation of Related Structures:  
    6FOX, 6FOY, 6FOZ, 6FP0, 6FP1, 6FPH

  • PubMed Abstract: 

    • Dysregulation of the kynurenine pathway (KP) leads to imbalances in neuroactive metabolites associated with the pathogenesis of several neurodegenerative disorders, including Huntington's disease (HD). Inhibition of the enzyme kynurenine 3-monooxygenase (KMO) in the KP normalises these metabolic imbalances and ameliorates neurodegeneration and related phenotypes in several neurodegenerative disease models ...

    Dysregulation of the kynurenine pathway (KP) leads to imbalances in neuroactive metabolites associated with the pathogenesis of several neurodegenerative disorders, including Huntington's disease (HD). Inhibition of the enzyme kynurenine 3-monooxygenase (KMO) in the KP normalises these metabolic imbalances and ameliorates neurodegeneration and related phenotypes in several neurodegenerative disease models. KMO is thus a promising candidate drug target for these disorders, but known inhibitors are not brain permeable. Here, 19 new KMO inhibitors have been identified. One of these ( 1 ) is neuroprotective in a Drosophila HD model but is minimally brain penetrant in mice. The prodrug variant ( 1b ) crosses the blood-brain barrier, releases 1 in the brain, thereby lowering levels of 3-hydroxykynurenine, a toxic KP metabolite linked to neurodegeneration. Prodrug 1b will advance development of targeted therapies against multiple neurodegenerative and neuroinflammatory diseases in which KP likely plays a role, including HD, Alzheimer's disease, and Parkinson's disease.

    Organizational Affiliation: 

    1Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN UK.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kynurenine 3-monooxygenase
A, B
460Pseudomonas fluorescensMutation(s): 0 
Gene Names: kmo, qbsG
EC: 1.14.13.9
UniProt
Find proteins for Q84HF5 (Pseudomonas fluorescens)
Explore Q84HF5 
Go to UniProtKB:  Q84HF5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84HF5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
E0H (Subject of Investigation/LOI)
Query on E0H
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		5-(3,4-dichlorophenyl)furan-2-carboxylic acid
C11 H6 Cl2 O3
GNXLBNMHCYYSPU-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.54α = 90
b = 52.19β = 103.53
c = 136.21γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
xia2data reduction
xia2data scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P009042/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/R000093/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/J020192/1
Medical Research Council (United Kingdom)United KingdomMR/N00373X/1

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references