6YT2 | pdb_00006yt2

Crystal Structure of human monoamine oxidase B in complex with Diphenylene iodonium (DPI)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.224 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.188 (Depositor) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6YT2

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Diphenylene Iodonium Is a Noncovalent MAO Inhibitor: A Biochemical and Structural Analysis.

Iacovino, L.G.Reis, J.Mai, A.Binda, C.Mattevi, A.

(2020) ChemMedChem 15: 1394-1397

  • DOI: https://doi.org/10.1002/cmdc.202000264
  • Primary Citation Related Structures: 
    6YT2

  • PubMed Abstract: 

    Diphenylene iodonium (DPI) is known for its inhibitory activities against many flavin- and heme-dependent enzymes, and is often used as an NADPH oxidase inhibitor. We probed the efficacy of DPI on two well-known drug targets, the human monoamine oxidases MAO A and B. UV-visible spectrophotometry and steady-state kinetics experiments demonstrate that DPI acts as a competitive and reversible MAO inhibitor with K i values of 1.7 and 0.3 μM for MAO A and MAO B, respectively. Elucidation of the crystal structure of human MAO B bound to the inhibitor revealed that DPI binds deeply in the active-site cavity to establish multiple hydrophobic interactions with the surrounding side chains and the flavin. These data prove that DPI is a genuine MAO inhibitor and that the inhibition mechanism does not involve a reaction with the reduced flavin. This binding and inhibitory activity against the MAOs, two major reactive oxygen species (ROS)-producing enzymes, will have to be carefully considered when interpreting experiments that rely on DPI for target validation and chemical biology studies on ROS functions.


  • Organizational Affiliation
    • Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy.

Macromolecule Content 

  • Total Structure Weight: 120.4 kDa 
  • Atom Count: 8,733 
  • 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] B
A, B
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
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
PJW
(Subject of Investigation/LOI)

Query on PJW



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
benzo[b][1]benziodole
C12 H8 I
PEWVMQDYYUSPRM-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.224 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.188 (Depositor) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.486α = 90
b = 222.544β = 90
c = 85.567γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

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: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary