8CAK

Crystal structure of dehydrogenase domain of Cylindrospermum stagnale NADPH-Oxidase 5 (NOX5) in complex with M41


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Targeting ROS production through inhibition of NADPH oxidases.

Reis, J.Gorgulla, C.Massari, M.Marchese, S.Valente, S.Noce, B.Basile, L.Torner, R.Cox 3rd, H.Viennet, T.Yang, M.H.Ronan, M.M.Rees, M.G.Roth, J.A.Capasso, L.Nebbioso, A.Altucci, L.Mai, A.Arthanari, H.Mattevi, A.

(2023) Nat Chem Biol 19: 1540-1550

  • DOI: https://doi.org/10.1038/s41589-023-01457-5
  • Primary Citation of Related Structures:  
    8CAK, 8CAL, 8CAO, 8CAP, 8CB0

  • PubMed Abstract: 

    NADPH oxidases (NOXs) are transmembrane enzymes that are devoted to the production of reactive oxygen species (ROS). In cancers, dysregulation of NOX enzymes affects ROS production, leading to redox unbalance and tumor progression. Consequently, NOXs are a drug target for cancer therapeutics, although current therapies have off-target effects: there is a need for isoenzyme-selective inhibitors. Here, we describe fully validated human NOX inhibitors, obtained from an in silico screen, targeting the active site of Cylindrospermum stagnale NOX5 (csNOX5). The hits are validated by in vitro and in cellulo enzymatic and binding assays, and their binding modes to the dehydrogenase domain of csNOX5 studied via high-resolution crystal structures. A high-throughput screen in a panel of cancer cells shows activity in selected cancer cell lines and synergistic effects with KRAS modulators. Our work lays the foundation for the development of inhibitor-based methods for controlling the tightly regulated and highly localized ROS sources.


  • Organizational Affiliation

    Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ferric reductase283Cylindrospermum stagnale BEA 0605BMutation(s): 0 
Gene Names: Cylst_1289
UniProt
Find proteins for K9WT99 (Cylindrospermum stagnale PCC 7417)
Explore K9WT99 
Go to UniProtKB:  K9WT99
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9WT99
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
U4F (Subject of Investigation/LOI)
Query on U4F

Download Ideal Coordinates CCD File 
C [auth A]15-(1,4-dioxa-8-azaspiro[4.5]decan-8-yl)-14-azatetracyclo[7.7.1.0^{2,7}.0^{13,17}]heptadeca-1(16),2(7),3,5,9,11,13(17),14-octaen-8-one
C23 H20 N2 O3
WRRCVQZTYRSVQE-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
F [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.476α = 90
b = 127.476β = 90
c = 71.944γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItalyIG19808
Italian Association for Cancer ResearchItaly800924

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release
  • Version 1.1: 2024-04-10
    Changes: Database references