9R3J | pdb_00009r3j

Crystal structure of human MAO B in complex with (E)-3-(benzo[d][1,3]dioxol-5-yl)-1-(3-(trifluoromethyl)phenyl)prop-2-en-1-one (chalcone inhibitor, 4e)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.172 (Depositor), 0.181 (DCC) 
  • R-Value Work: 
    0.150 (Depositor), 0.162 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Design, synthesis, and biological evaluation of chalcone derivatives as selective Monoamine Oxidase-B inhibitors with potential neuroprotective effects.

Facchetti, G.Marchese, S.Cocce, V.Doneda, L.Alessandri, G.Paino, F.Pessina, A.Pinzi, L.Rastelli, G.Binda, C.Christodoulou, M.S.Rimoldi, I.

(2025) Eur J Med Chem 298: 117990-117990

  • DOI: https://doi.org/10.1016/j.ejmech.2025.117990
  • Primary Citation Related Structures: 
    9R2J, 9R3J, 9R3K

  • PubMed Abstract: 

    A series of chalcone derivatives was synthesized via Claisen-Schmidt condensation and further modified through selective reductions and amide couplings to explore their potential as monoamine oxidase B (MAO-B) inhibitors. Screening against recombinant human MAO-B identified compounds 4a, 4b, 4e, and 5a as potent inhibitors, showing submicromolar inhibition constants (K i ). Structure-activity relationship (SAR) analysis emphasized the relevance of a planar α,β-unsaturated carbonyl and specific aromatic substitutions for activity. Crystallographic studies showed conserved binding modes in the MAO-B active site, while computational analyses confirmed favourable interactions and conformational flexibility of compound 5a. Cytotoxicity assays in normal and cancer cell lines indicated minimal toxicity for 5a. Notably, 5a also exhibited neuroprotective effects in SH-SY5Y cells exposed to 6-hydroxydopamine (6-OHDA), a model of Parkinson's disease. These findings demonstrated the importance of structural fine-tuning within the chalcone scaffold to achieve MAO-B selectivity and identify compound 5a as a promising, non-toxic candidate for neurodegenerative disease treatment.


  • Organizational Affiliation
    • CRC StaMeTec, Department of Pharmaceutical Science, University of Milan, Via Golgi 19, 20133, Milan, Italy.

Macromolecule Content 

  • Total Structure Weight: 120.3 kDa 
  • Atom Count: 9,010 
  • Modeled Residue Count: 995 
  • Deposited Residue Count: 1,038 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Amine oxidase [flavin-containing] BA [auth AAA],
B [auth BBB]
519Homo sapiensMutation(s): 0 
Gene Names: MAOB
EC: 1.4.3.4 (PDB Primary Data), 1.4.3.21 (UniProt)
Membrane Entity: Yes 
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
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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
C15

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
A1JC8
(Subject of Investigation/LOI)

Query on A1JC8



Download:Ideal Coordinates CCD File
E [auth AAA],
H [auth BBB]
(~{E})-3-(1,3-benzodioxol-5-yl)-1-[3-(trifluoromethyl)phenyl]prop-2-en-1-one
C17 H11 F3 O3
FQIMIDFHNGYPLI-GQCTYLIASA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.172 (Depositor), 0.181 (DCC) 
  • R-Value Work:  0.150 (Depositor), 0.162 (DCC) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.299α = 90
b = 222.293β = 90
c = 86.211γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Ministry of EducationItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release