Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 120.70 kDa 
• Atom Count: 9179 
• Modelled Residue Count: 995 
• Deposited Residue Count: 1040 
• Unique protein chains: 1

6FW0

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

• PDB DOI: 10.2210/pdb6FW0/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2018-03-05 Released: 2018-04-25 
• Deposition Author(s): Reis, J., Manzella, N., Cagide, F., Mialet-Perez, J., Uriarte, E., Parini, A., Borges, F., Binda, C.
• Funding Organization(s): Fondazione Cariplo

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.191 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

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

• PubMed: 29648817 
• DOI: 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).

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Organizational Affiliation: 

Department of Biology and Biotechnology , University of Pavia , 27100 Pavia , Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amine oxidase [flavin-containing] B	A, B	520	Homo sapiens	Mutation(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
PHAROS:  P27338 GTEx:  ENSG00000069535

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], G [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
C15	E [auth A], I [auth B]	N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE C17 H38 N O3 S IZWSFJTYBVKZNK-UHFFFAOYSA-O
E92	D [auth A], H [auth B]	~{N}-(3-chlorophenyl)-4-oxidanylidene-chromene-3-carboxamide C16 H10 Cl N O3 CVLFPXGWUQAEEW-UHFFFAOYSA-N
GOL	F [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
E92	BindingDB:  6FW0	Ki: min: 0.79, max: 17 (nM) from 3 assay(s)
		IC50: min: 0.4, max: 0.41 (nM) from 2 assay(s)
	Binding MOAD:  6FW0	Ki: 17 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.191 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.41	α = 90
b = 221.991	β = 90
c = 86.106	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-03-05 
• Released Date: 2018-04-25 
Deposition Author(s): Reis, J., Manzella, N., Cagide, F., Mialet-Perez, J., Uriarte, E., Parini, A., Borges, F., Binda, C.

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Funding Organization	Location	Grant Number
Fondazione Cariplo	Italy	2014-0672

Revision History  

• Version 1.0: 2018-04-25
  Type: Initial release
  
• Version 1.1: 2018-05-23
  Changes: Data collection, Database references