7K12

ACMSD in complex with diflunisal

  • Classification: LYASE
  • Organism(s): Pseudomonas fluorescens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2020-09-07 Released: 2021-01-13 
  • Deposition Author(s): Yang, Y., Liu, A.
  • Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Diflunisal Derivatives as Modulators of ACMS Decarboxylase Targeting the Tryptophan-Kynurenine Pathway.

Yang, Y.Borel, T.de Azambuja, F.Johnson, D.Sorrentino, J.P.Udokwu, C.Davis, I.Liu, A.Altman, R.A.

(2021) J Med Chem 64: 797-811

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01762
  • Primary Citation of Related Structures:  
    7K12, 7K13

  • PubMed Abstract: 

    In the kynurenine pathway for tryptophan degradation, an unstable metabolic intermediate, α-amino-β-carboxymuconate-ε-semialdehyde (ACMS), can nonenzymatically cyclize to form quinolinic acid, the precursor for de novo biosynthesis of nicotinamide adenine dinucleotide (NAD + ). In a competing reaction, ACMS is decarboxylated by ACMS decarboxylase (ACMSD) for further metabolism and energy production. Therefore, the inhibition of ACMSD increases NAD + levels. In this study, an Food and Drug Administration (FDA)-approved drug, diflunisal, was found to competitively inhibit ACMSD. The complex structure of ACMSD with diflunisal revealed a previously unknown ligand-binding mode and was consistent with the results of inhibition assays, as well as a structure-activity relationship (SAR) study. Moreover, two synthesized diflunisal derivatives showed half-maximal inhibitory concentration (IC 50 ) values 1 order of magnitude better than diflunisal at 1.32 ± 0.07 μM ( 22 ) and 3.10 ± 0.11 μM ( 20 ), respectively. The results suggest that diflunisal derivatives have the potential to modulate NAD + levels. The ligand-binding mode revealed here provides a new direction for developing inhibitors of ACMSD.


  • Organizational Affiliation

    Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
A, B
355Pseudomonas fluorescensMutation(s): 0 
Gene Names: nbaD
EC: 4
UniProt
Find proteins for Q83V25 (Pseudomonas fluorescens)
Explore Q83V25 
Go to UniProtKB:  Q83V25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ83V25
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.588α = 90
b = 93.588β = 90
c = 445.743γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1623856
National Science Foundation (NSF, United States)United StatesCHE-1808637
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM108988
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM133721
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesMH107985

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description