Rasagiline-inhibited human monoamine oxidase B in complex with 2-(2- benzofuranyl)-2-imidazoline

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Work: 0.159 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


Potentiation of ligand binding through cooperative effects in monoamine oxidase B.

Bonivento, D.Milczek, E.M.McDonald, G.R.Binda, C.Holt, A.Edmondson, D.E.Mattevi, A.

(2010) J Biol Chem 285: 36849-36856

  • DOI: https://doi.org/10.1074/jbc.M110.169482
  • Primary Citation of Related Structures:  
    2XCG, 2XFN, 2XFO, 2XFP, 2XFQ, 2XFU

  • PubMed Abstract: 

    Crystallographic and biochemical studies have been employed to identify the binding site and mechanism for potentiation of imidazoline binding in human monoamine oxidase B (MAO B). 2-(2-Benzofuranyl)-2-imidazoline (2-BFI) inhibits recombinant human MAO B with a K(i) of 8.3 ± 0.6 μM, whereas tranylcypromine-inhibited MAO B binds 2-BFI with a K(d) of 9 ± 2 nM, representing an increase in binding energy Δ(ΔG) of -3.9 kcal/mol. Crystal structures show the imidazoline ligand bound in a site that is distinct from the substrate-binding cavity. Contributions to account for the increase in binding affinity upon tranylcypromine inhibition include a conformational change in the side chain of Gln(206) and a "closed conformation" of the side chain of Ile(199), forming a hydrophobic "sandwich" with the side chain of Ile(316) on each face of the benzofuran ring of 2-BFI. Data with the I199A mutant of human MAO B and failure to observe a similar binding potentiation with rat MAO B, where Ile(316) is replaced with a Val residue, support an allosteric mechanism where the increased binding affinity of 2-BFI results from a cooperative increase in H-bond strength through formation of a more hydrophobic milieu. These insights should prove valuable in the design of high affinity and specific reversible MAO B inhibitors.

  • Organizational Affiliation

    Department of Genetics and Microbiology, University of Pavia, I-27100 Pavia PV, Italy.

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
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
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
C27 H33 N9 O15 P2
Query on C15

Download Ideal Coordinates CCD File 
C17 H38 N O3 S
Query on XCG

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
C11 H8 N2 O
Query on RAS

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
C12 H15 N
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Work: 0.159 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.51α = 90
b = 223.38β = 90
c = 86.55γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2012-02-29
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-12-20
    Changes: Database references
  • Version 1.3: 2018-05-16
    Changes: Data collection
  • Version 1.4: 2018-10-17
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary