2V60

Structure of human MAO B in complex with the selective inhibitor 7-(3- chlorobenzyloxy)-4-carboxaldehyde-coumarin

• PDB DOI: https://doi.org/10.2210/pdb2V60/pdb

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


• Deposited: 2007-07-12 Released: 2007-10-16 
• Deposition Author(s): Binda, C., Wang, J., Pisani, L., Caccia, C., Carotti, A., Salvati, P., Edmondson, D.E., Mattevi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.221 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Starting Model: experimental

Literature

Structures of Human Monoamine Oxidase B Complexes with Selective Noncovalent Inhibitors: Safinamide and Coumarin Analogs.

Binda, C., Wang, J., Pisani, L., Caccia, C., Carotti, A., Salvati, P., Edmondson, D.E., Mattevi, A.

(2007) J Med Chem 50: 5848

• PubMed: 17915852 
• DOI: https://doi.org/10.1021/jm070677y
• Primary Citation of Related Structures:  
  2V5Z, 2V60, 2V61


• PubMed Abstract: 
  

  Structures of human monoamine oxidase B (MAO B) in complex with safinamide and two coumarin derivatives, all sharing a common benzyloxy substituent, were determined by X-ray crystallography. These compounds competitively inhibit MAO B with Ki values in the 0.1-0.5 microM range that are 30-700-fold lower than those observed with MAO A. The inhibitors bind noncovalently to MAO B, occupying both the entrance and the substrate cavities and showing a similarly oriented benzyloxy substituent.

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Organizational Affiliation: 

Department of Genetics and Microbiology, University of Pavia, via Ferrata 1, Pavia, 27100 Italy.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 119.88 kDa 
• Atom Count: 8,817 
• Modelled Residue Count: 993 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMINE OXIDASE (FLAVIN-CONTAINING) B	A, B	520	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
C17	D [auth A], F [auth B]	7-[(3-CHLOROBENZYL)OXY]-2-OXO-2H-CHROMENE-4-CARBALDEHYDE C17 H11 Cl O4 ZOCADHRNWNJARU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
C17	BindingDB:  2V60	Ki: 400 (nM) from 1 assay(s)
		IC50: 52 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.221 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.694	α = 90
b = 224.413	β = 90
c = 86.811	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-16 
Deposition Author(s): Binda, C., Wang, J., Pisani, L., Caccia, C., Carotti, A., Salvati, P., Edmondson, D.E., Mattevi, A.

Revision History  

• Version 1.0: 2007-10-16
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary