6FVZ

Crystal structure of human monoamine oxidase B (MAO B) in complex with dimethylphenyl-chromone-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Tight-Binding Inhibition of Human Monoamine Oxidase B by Chromone Analogs: A Kinetic, Crystallographic, and Biological Analysis.

Reis, J.Manzella, N.Cagide, F.Mialet-Perez, J.Uriarte, E.Parini, A.Borges, F.Binda, C.

(2018) J Med Chem 61: 4203-4212

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00357
  • Primary Citation of Related Structures:  
    6FVZ, 6FW0, 6FWC

  • PubMed Abstract: 

    Monoamine oxidase B (MAO-B) is a validated drug target for Parkinson's disease. Chromone derivatives were identified as novel potent and reversible MAO-B inhibitors, and herewith we report on a crystallographic and biochemical analysis to investigate their inhibition mechanism. The crystal structures of human MAO-B in complex with three chromone analogs bearing different substituents on the exocyclic aromatic ring (determined at 1.6-1.8 Å resolution) showed that they all bind in the active site cavity of the protein with the chromone moiety located in front of the FAD cofactor. These inhibitors form two hydrogen bonds with Tyr435 and Cys172 and perfectly fit the hydrophobic flat active site of human MAO-B. This is reflected in their tight-binding mechanism of inhibition with K i values of 55, 17, and 31 nM for N-(3',4'-dimethylphenyl)-4-oxo-4 H-chromene-3-carboxamide (1), N-(3'-chlorophenyl)-4-oxo-4 H-chromene-3-carboxamide (2), and N-(3'-fluorophenyl)-4-oxo-4 H-chromene-3-carboxamide (3), respectively. These compounds were also 1000-fold more effective than l-deprenyl in reducing the cellular levels of reactive oxygen species (ROS).


  • Organizational Affiliation

    CIQUP/Department of Chemistry and Biochemistry , University of Porto , 4169-007 Porto , Portugal.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amine oxidase [flavin-containing] B
A, B
520Homo sapiensMutation(s): 0 
Gene Names: MAOB
EC: 1.4.3.4
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P27338 (Homo sapiens)
Explore P27338 
Go to UniProtKB:  P27338
GTEx:  ENSG00000069535 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27338
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 
C [auth A],
G [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
C15
Query on C15

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE
C17 H38 N O3 S
IZWSFJTYBVKZNK-UHFFFAOYSA-O
E8Z
Query on E8Z

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
~{N}-(3,4-dimethylphenyl)-4-oxidanylidene-chromene-3-carboxamide
C18 H15 N O3
WDCZOLPCRVTBPH-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
E8Z Binding MOAD:  6FVZ Ki: 55 (nM) from 1 assay(s)
BindingDB:  6FVZ Ki: min: 0.31, max: 55 (nM) from 3 assay(s)
IC50: min: 0.67, max: 0.68 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.182α = 90
b = 222.753β = 90
c = 86.482γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fondazione CARIPLOItaly2014-0672

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.2: 2020-04-22
    Changes: Author supporting evidence, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description