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- PDB-9fjt: Human Monoamine Oxidase B in complex with MC4762 inhibitor (9a) a... -

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Basic information

Entry
Database: PDB / ID: 9fjt
TitleHuman Monoamine Oxidase B in complex with MC4762 inhibitor (9a) at 1.4 A resolution
ComponentsAmine oxidase [flavin-containing] B
KeywordsFLAVOPROTEIN / MAO / amine oxidase / oxidase
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: 1.4 Å
AuthorsGottinger, A. / Binda, C.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca Italy
CitationJournal: J.Med.Chem. / Year: 2025
Title: Design of Benzyl-triazolopyrimidine-Based NADPH Oxidase Inhibitors Leads to the Discovery of a Potent Dual Covalent NOX2/MAOB Inhibitor.
Authors: Noce, B. / Marchese, S. / Massari, M. / Lambona, C. / Reis, J. / Fiorentino, F. / Raucci, A. / Fioravanti, R. / Casteloa, M. / Mormino, A. / Garofalo, S. / Limatola, C. / Basile, L. / ...Authors: Noce, B. / Marchese, S. / Massari, M. / Lambona, C. / Reis, J. / Fiorentino, F. / Raucci, A. / Fioravanti, R. / Casteloa, M. / Mormino, A. / Garofalo, S. / Limatola, C. / Basile, L. / Gottinger, A. / Binda, C. / Mattevi, A. / Mai, A. / Valente, S.
History
DepositionMay 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)120,8038
Polymers117,6752
Non-polymers3,1276
Water17,529973
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9290 Å2
ΔGint-34 kcal/mol
Surface area35630 Å2
Unit cell
Length a, b, c (Å)130.920, 222.033, 85.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

#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
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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1IDI / ~{N}-[[4-[[7-(1,3-benzoxazol-2-ylsulfanyl)-[1,2,3]triazolo[4,5-d]pyrimidin-3-yl]methyl]phenyl]methyl]-~{N}-methyl-prop-2-yn-1-amine


Mass: 441.508 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H19N7OS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 973 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12 % (w/v) PEG 4000, 100 mM ADA buffer pH 6.5, 70 mM Lithium Sulfate, 4.5 mM Zwittergent 3-12

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.4→47.18 Å / Num. obs: 243584 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.081 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 12035 / CC1/2: 0.627 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→47.18 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.031 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.053
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1899 6176 2.537 %
Rwork0.1667 237295 -
all0.167 --
obs-243471 99.706 %
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: 15.064 Å2
Baniso -1Baniso -2Baniso -3
1-0.585 Å20 Å2-0 Å2
2---0.428 Å20 Å2
3----0.157 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7911 0 187 973 9071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0138400
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177945
X-RAY DIFFRACTIONr_angle_refined_deg1.931.68311438
X-RAY DIFFRACTIONr_angle_other_deg1.9331.59118343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49751021
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33621.651418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.679151441
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg19.871152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4881558
X-RAY DIFFRACTIONr_chiral_restr0.1060.21063
X-RAY DIFFRACTIONr_chiral_restr_other0.0680.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.029276
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021865
X-RAY DIFFRACTIONr_nbd_refined0.2310.21833
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.28002
X-RAY DIFFRACTIONr_nbtor_refined0.1820.24158
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.23869
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2678
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.070.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0960.27
X-RAY DIFFRACTIONr_nbd_other0.3380.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.219
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_mcbond_it1.3581.3114000
X-RAY DIFFRACTIONr_mcbond_other1.3561.3093999
X-RAY DIFFRACTIONr_mcangle_it1.9421.9645004
X-RAY DIFFRACTIONr_mcangle_other1.9421.9655005
X-RAY DIFFRACTIONr_scbond_it2.7971.6494399
X-RAY DIFFRACTIONr_scbond_other2.7971.6494400
X-RAY DIFFRACTIONr_scangle_it4.2082.3636419
X-RAY DIFFRACTIONr_scangle_other4.2082.3636420
X-RAY DIFFRACTIONr_lrange_it5.38726.60438225
X-RAY DIFFRACTIONr_lrange_other5.22526.04237200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.2754480.26517502X-RAY DIFFRACTION99.9276
1.436-1.4760.3254060.30417016X-RAY DIFFRACTION99.7538
1.476-1.5180.284170.2716549X-RAY DIFFRACTION99.6652
1.518-1.5650.2444400.2316043X-RAY DIFFRACTION99.7458
1.565-1.6170.23990.17615600X-RAY DIFFRACTION99.95
1.617-1.6730.1943900.17115076X-RAY DIFFRACTION99.9225
1.673-1.7360.193930.16914582X-RAY DIFFRACTION99.9133
1.736-1.8070.1773640.14814034X-RAY DIFFRACTION99.9514
1.807-1.8880.1763430.15313516X-RAY DIFFRACTION99.9351
1.888-1.980.2483540.19112782X-RAY DIFFRACTION99.2145
1.98-2.0870.1763150.17412167X-RAY DIFFRACTION98.9771
2.087-2.2130.1623000.13811645X-RAY DIFFRACTION99.9916
2.213-2.3660.1642760.14110830X-RAY DIFFRACTION99.0546
2.366-2.5560.152780.12810202X-RAY DIFFRACTION99.9428
2.556-2.7990.1632720.1389363X-RAY DIFFRACTION99.5969
2.799-3.130.1542030.1388543X-RAY DIFFRACTION99.8402
3.13-3.6130.1581930.1467517X-RAY DIFFRACTION99.2278
3.613-4.4240.1651730.1446415X-RAY DIFFRACTION99.6069
4.424-6.2520.1921400.1695029X-RAY DIFFRACTION99.9613
6.252-47.180.312720.2072885X-RAY DIFFRACTION99.1284

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