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- PDB-9r3j: Crystal structure of human MAO B in complex with (E)-3-(benzo[d][... -

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Basic information

Entry
Database: PDB / ID: 9r3j
TitleCrystal structure of human MAO B in complex with (E)-3-(benzo[d][1,3]dioxol-5-yl)-1-(3-(trifluoromethyl)phenyl)prop-2-en-1-one (chalcone inhibitor, 4e)
ComponentsAmine oxidase [flavin-containing] B
KeywordsFLAVOPROTEIN / monoamine oxidase / chalcone / neuroprotective drug
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: 1.7 Å
AuthorsMarchese, S. / Binda, C.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Design, synthesis, and biological evaluation of chalcone derivatives as selective Monoamine Oxidase-B inhibitors with potential neuroprotective effects.
Authors: Facchetti, G. / Marchese, S. / Cocce, V. / Doneda, L. / Alessandri, G. / Paino, F. / Pessina, A. / Pinzi, L. / Rastelli, G. / Binda, C. / Christodoulou, M.S. / Rimoldi, I.
History
DepositionMay 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)120,2988
Polymers117,4132
Non-polymers2,8856
Water15,835879
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-33 kcal/mol
Surface area36260 Å2
Unit cell
Length a, b, c (Å)131.299, 222.293, 86.211
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11AAA-1112-

HOH

21BBB-811-

HOH

31BBB-820-

HOH

41BBB-997-

HOH

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Components

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


Mass: 58706.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAOB / Production host: Komagataella pastoris (fungus) / References: UniProt: P27338, monoamine oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: 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
#4: Chemical ChemComp-A1JC8 / (~{E})-3-(1,3-benzodioxol-5-yl)-1-[3-(trifluoromethyl)phenyl]prop-2-en-1-one


Mass: 320.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H11F3O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 879 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% PEG4000, 100 mM ADA pH 6.5, 70 mM lithium sulphate, 8.5 mM Zwittergent 3-12

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.7→47.27 Å / Num. obs: 138049 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Rrim(I) all: 0.085 / Net I/σ(I): 16.4
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.601 / Num. unique obs: 6764 / CC1/2: 0.83 / Rpim(I) all: 0.38 / Rrim(I) all: 0.714

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.27 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.559 / SU ML: 0.051 / Cross valid method: FREE R-VALUE / ESU R: 0.078 / ESU R Free: 0.077
RfactorNum. reflection% reflection
Rfree0.1725 3453 2.501 %
Rwork0.1498 134585 -
all0.15 --
obs-138038 99.901 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.865 Å20 Å20 Å2
2---0.718 Å20 Å2
3----0.147 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7926 0 178 879 8983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0138344
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177887
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.6811355
X-RAY DIFFRACTIONr_angle_other_deg1.8811.58918191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53351003
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25721.524420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21151422
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg19.43152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9581560
X-RAY DIFFRACTIONr_chiral_restr0.1640.21059
X-RAY DIFFRACTIONr_chiral_restr_other0.0490.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.029204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021862
X-RAY DIFFRACTIONr_nbd_refined0.2140.21640
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.27605
X-RAY DIFFRACTIONr_nbtor_refined0.1770.24059
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.23691
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2660
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1870.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1520.28
X-RAY DIFFRACTIONr_nbd_other0.2050.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.218
X-RAY DIFFRACTIONr_mcbond_it1.6451.6933988
X-RAY DIFFRACTIONr_mcbond_other1.6381.6923987
X-RAY DIFFRACTIONr_mcangle_it2.2562.5324984
X-RAY DIFFRACTIONr_mcangle_other2.2582.5334985
X-RAY DIFFRACTIONr_scbond_it3.182.064356
X-RAY DIFFRACTIONr_scbond_other3.182.064357
X-RAY DIFFRACTIONr_scangle_it4.7272.9536366
X-RAY DIFFRACTIONr_scangle_other4.7272.9536367
X-RAY DIFFRACTIONr_lrange_it5.8221.039731
X-RAY DIFFRACTIONr_lrange_other5.67220.4899513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.2262350.29888X-RAY DIFFRACTION99.8028
1.744-1.7920.2082630.1789600X-RAY DIFFRACTION100
1.792-1.8440.1932490.1699347X-RAY DIFFRACTION99.9896
1.844-1.9010.1922200.1689118X-RAY DIFFRACTION99.9572
1.901-1.9630.1842110.178845X-RAY DIFFRACTION99.8677
1.963-2.0320.1742120.1428516X-RAY DIFFRACTION100
2.032-2.1090.1662040.1468259X-RAY DIFFRACTION99.8702
2.109-2.1950.1661980.1347964X-RAY DIFFRACTION99.9633
2.195-2.2920.1711930.1397600X-RAY DIFFRACTION99.7823
2.292-2.4040.1481880.1267297X-RAY DIFFRACTION100
2.404-2.5340.151950.1316978X-RAY DIFFRACTION100
2.534-2.6880.1521800.1336565X-RAY DIFFRACTION99.9555
2.688-2.8730.1581750.1356179X-RAY DIFFRACTION99.9685
2.873-3.1030.1631350.1425791X-RAY DIFFRACTION99.9831
3.103-3.3990.1551330.1475325X-RAY DIFFRACTION99.9634
3.399-3.80.1731350.1554837X-RAY DIFFRACTION99.8394
3.8-4.3870.1481080.1354296X-RAY DIFFRACTION99.8639
4.387-5.3710.1811000.1493665X-RAY DIFFRACTION99.9469

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