9FJT

Human Monoamine Oxidase B in complex with MC4762 inhibitor (9a) at 1.4 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.190 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.176 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view detailsBest fitted C15Click on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

Design of Benzyl-triazolopyrimidine-Based NADPH Oxidase Inhibitors Leads to the Discovery of a Potent Dual Covalent NOX2/MAOB Inhibitor.

Noce, B.Marchese, S.Massari, M.Lambona, C.Reis, J.Fiorentino, F.Raucci, A.Fioravanti, R.Casteloa, M.Mormino, A.Garofalo, S.Limatola, C.Basile, L.Gottinger, A.Binda, C.Mattevi, A.Mai, A.Valente, S.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02644
  • Primary Citation of Related Structures:  
    9FJT

  • PubMed Abstract: 

    NADPH oxidases (NOXs) are enzymes dedicated to reactive oxygen species (ROS) production and are implicated in cancer, neuroinflammation, and neurodegenerative diseases. VAS2870 is a covalent inhibitor of mainly NOX2 and NOX5. It alkylates a conserved active-site cysteine, blocking productive substrate binding. To enhance potency and selectivity toward NOXs, we conducted some chemical modifications, leading to the discovery of compound 9a that preferentially inhibits NOX2 with an IC 50 of 0.155 μM, and only upon its preactivation. We found that 9a , bearing a pargyline moiety, is also able to selectively inhibit MAOB over MAOA (465-fold) with an IC 50 of 0.182 μM, being the first-in-class dual NOX2/MAOB covalent inhibitor. Tested in the BV2 microglia neuroinflammation model, 9a decreased ROS production and downregulated proinflammatory cytokines as iNOS, IL-1β, and IL-6 expression more efficiently than the single target inhibitors (rasagiline for MAOB and VAS2870 for NOXs) but also, more importantly, than their combination.


  • Organizational Affiliation

    Department of Drug Chemistry and Technologies, Sapienza University of Rome, P.le Aldo Moro 5, Rome 00185, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amine oxidase [flavin-containing] BA [auth AAA],
B [auth BBB]
520Homo sapiensMutation(s): 0 
Gene Names: MAOB
EC: 1.4.3.4 (PDB Primary Data), 1.4.3.21 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P27338 (Homo sapiens)
Explore P27338 
Go to UniProtKB:  P27338
PHAROS:  P27338
GTEx:  ENSG00000069535 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27338
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth AAA],
F [auth BBB]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
A1IDI (Subject of Investigation/LOI)
Query on A1IDI

Download Ideal Coordinates CCD File 
E [auth AAA],
H [auth BBB]
~{N}-[[4-[[7-(1,3-benzoxazol-2-ylsulfanyl)-[1,2,3]triazolo[4,5-d]pyrimidin-3-yl]methyl]phenyl]methyl]-~{N}-methyl-prop-2-yn-1-amine
C23 H19 N7 O S
BQRUEJOUZILBFB-UHFFFAOYSA-N
C15 (Subject of Investigation/LOI)
Query on C15

Download Ideal Coordinates CCD File 
D [auth AAA],
G [auth BBB]
N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE
C17 H38 N O3 S
IZWSFJTYBVKZNK-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.190 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.176 (DCC) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.92α = 90
b = 222.033β = 90
c = 85.879γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view detailsBest fitted C15Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministero dell Universita e della RicercaItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release