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- PDB-28wl: Crystal structure of human Monoamine Oxidase B (MAO B) in complex... -

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Basic information

Entry
Database: PDB / ID: 28wl
TitleCrystal structure of human Monoamine Oxidase B (MAO B) in complex with 7-[(4-{[(3,4-dimethoxybenzyl(methyl)amino]methyl}benzyl)oxy]-4-(hydroxymethyl)-2H-chromen-2-one) (LP1488)
ComponentsAmine oxidase [flavin-containing] B
KeywordsFLAVOPROTEIN / monoamine oxidase / inhibitor / drug design / Alzheimer / multitarget
Function / homology
Function and homology information


Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / primary-amine oxidase / primary methylamine oxidase activity / dopamine catabolic process / mitochondrial envelope / hydrogen peroxide biosynthetic process / substantia nigra development / flavin adenine dinucleotide binding ...Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / primary-amine oxidase / primary methylamine oxidase activity / dopamine catabolic process / mitochondrial envelope / hydrogen peroxide biosynthetic process / substantia nigra development / flavin adenine dinucleotide binding / mitochondrial outer membrane / electron transfer activity / mitochondrion
Similarity search - Function
: / Flavin amine oxidase / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / Chem-C15 / FLAVIN-ADENINE DINUCLEOTIDE / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMarchese, S. / Gottinger, A. / Pisani, L. / Binda, C.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education2022LWZ77N Italy
CitationJournal: Eur.J.Med.Chem. / Year: 2026
Title: Leveraging multitargeting BChE-MAO B inhibitors against microglia-related neuroinflammation: in vitro biological evaluation, structure-activity relationships, drug-like properties, and X-ray crystal complexes
Authors: Rullo, M. / La Spada, G. / Brazzolotto, X. / Marchese, S. / El Idrissi, I.G. / Miciaccia, M. / Colella, M. / Brea, J.M. / Macchia, E. / Loza, M.I. / Gottinger, A. / Scilimati, A. / Perrone, ...Authors: Rullo, M. / La Spada, G. / Brazzolotto, X. / Marchese, S. / El Idrissi, I.G. / Miciaccia, M. / Colella, M. / Brea, J.M. / Macchia, E. / Loza, M.I. / Gottinger, A. / Scilimati, A. / Perrone, M.G. / Stefanachi, A. / Binda, C. / Leonetti, F. / Pisani, L.
History
DepositionFeb 24, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amine oxidase [flavin-containing] B
B: Amine oxidase [flavin-containing] B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,14711
Polymers117,6752
Non-polymers3,4729
Water14,952830
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)130.599, 222.270, 85.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-1072-

HOH

21B-866-

HOH

31B-892-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Amine oxidase [flavin-containing] B / Monoamine oxidase type B / MAO-B


Mass: 58837.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The last 19 residues are not visible in the electron density map.
Source: (gene. exp.) Homo sapiens (human) / Gene: MAOB / Production host: Komagataella pastoris (fungus) / References: UniProt: P27338, monoamine oxidase

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Non-polymers , 5 types, 839 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-A1JF0 / 7-[[4-[[(3,4-dimethoxyphenyl)methyl-methyl-amino]methyl]phenyl]methoxy]-4-(hydroxymethyl)chromen-2-one


Mass: 475.533 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H29NO6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-C15 / N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE


Mass: 336.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H38NO3S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 830 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% PEG4000, 100 mM ADA buffer pH 6.5, 70 mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96546 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 29, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.6→86.1 Å / Num. obs: 164045 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 12.158 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.055 / Rrim(I) all: 0.102 / Net I/σ(I): 16.1
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 1.048 / Mean I/σ(I) obs: 2 / Num. unique obs: 8084 / CC1/2: 0.605 / Rpim(I) all: 0.661 / Rrim(I) all: 1.243

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→86.1 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.487 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.183 4158 2.5 %RANDOM
Rwork0.15252 ---
obs0.1533 159877 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.845 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2---0.66 Å20 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.6→86.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7926 0 194 830 8950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0138351
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177902
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.67111357
X-RAY DIFFRACTIONr_angle_other_deg1.8781.58418229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58451003
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.00421.655417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.873151420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0881558
X-RAY DIFFRACTIONr_chiral_restr0.0970.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.029196
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021852
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4981.6083988
X-RAY DIFFRACTIONr_mcbond_other1.4961.6073987
X-RAY DIFFRACTIONr_mcangle_it2.0722.4064984
X-RAY DIFFRACTIONr_mcangle_other2.0722.4074985
X-RAY DIFFRACTIONr_scbond_it2.9191.9544363
X-RAY DIFFRACTIONr_scbond_other2.9191.9544364
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3932.8066369
X-RAY DIFFRACTIONr_long_range_B_refined5.33120.0949758
X-RAY DIFFRACTIONr_long_range_B_other5.1919.6389568
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 279 -
Rwork0.257 11740 -
obs--99.98 %

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