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- PDB-7nbm: Co-crystal structure of Human Nicotinamide N-methyltransferase (N... -

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Basic information

Entry
Database: PDB / ID: 7nbm
TitleCo-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with the bisubstrate-like inhibitor (33)
ComponentsNicotinamide N-methyltransferase
KeywordsTRANSFERASE / Methyl Transferase / drug discovery / Inhibitor complex / Nicotinamide / metabolic disorders
Function / homology
Function and homology information


pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide N-methyltransferase activity / nicotinamide metabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / : / positive regulation of protein deacetylation / Methylation / Nicotinamide salvage / animal organ regeneration ...pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide N-methyltransferase activity / nicotinamide metabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / : / positive regulation of protein deacetylation / Methylation / Nicotinamide salvage / animal organ regeneration / positive regulation of gluconeogenesis / methylation / response to xenobiotic stimulus / cytosol
Similarity search - Function
Methyltransferase, NNMT/PNMT/TEMT / Methyltransferase NNMT/PNMT/TEMT, conserved site / : / NNMT/PNMT/TEMT family / NNMT/PNMT/TEMT family of methyltransferases signature. / SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-U7K / Nicotinamide N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.691 Å
AuthorsSchreuder, H.A. / Liesum, A.
CitationJournal: Molecules / Year: 2021
Title: Novel Inhibitors of Nicotinamide- N -Methyltransferase for the Treatment of Metabolic Disorders.
Authors: Kannt, A. / Rajagopal, S. / Hallur, M.S. / Swamy, I. / Kristam, R. / Dhakshinamoorthy, S. / Czech, J. / Zech, G. / Schreuder, H. / Ruf, S.
History
DepositionJan 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nicotinamide N-methyltransferase
B: Nicotinamide N-methyltransferase
C: Nicotinamide N-methyltransferase
D: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,8158
Polymers125,8644
Non-polymers1,9504
Water4,774265
1
A: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9542
Polymers31,4661
Non-polymers4881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9542
Polymers31,4661
Non-polymers4881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9542
Polymers31,4661
Non-polymers4881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9542
Polymers31,4661
Non-polymers4881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.301, 61.973, 108.197
Angle α, β, γ (deg.)92.48, 98.14, 111.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nicotinamide N-methyltransferase


Mass: 31466.033 Da / Num. of mol.: 4 / Mutation: K100A, E101A, E103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): DE
References: UniProt: P40261, nicotinamide N-methyltransferase
#2: Chemical
ChemComp-U7K / (E)-3-((5,6-dihydro-2H,4H-thiazolo[5,4,3-ij]quinolin-2-ylidene)amino)-2-hydroxy-1-(4-(isoquinolin-5-yl)piperazin-1-yl)-2-methylpropan-1-one / (2~{S})-1-(4-isoquinolin-5-ylpiperazin-1-yl)-2-methyl-2-oxidanyl-3-[(~{E})-3-thia-1-azatricyclo[6.3.1.0^{4,12}]dodeca-4(12),5,7-trien-2-ylideneamino]propan-1-one


Mass: 487.616 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H29N5O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Human NNMT was crystallized using the following conditions: A protein solution with 6 mg/ml NNMT, 50 mM Tris/HCL, pH 8.0, 1 mM DTT, 0.95mM inhibitor and 5% v/v glycerol was equilibrated at ...Details: Human NNMT was crystallized using the following conditions: A protein solution with 6 mg/ml NNMT, 50 mM Tris/HCL, pH 8.0, 1 mM DTT, 0.95mM inhibitor and 5% v/v glycerol was equilibrated at room temperature in a hanging drop setup against 2.2 M ammonium sulfate with 0.1 M HEPES/Na, pH 7.6. Small crystal appeared after 1-2 weeks.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.69→41.97 Å / Num. obs: 26311 / % possible obs: 88 % / Redundancy: 1.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.109 / Net I/σ(I): 7.2
Reflection shellResolution: 2.69→2.85 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3895 / CC1/2: 0.651 / Rrim(I) all: 0.684 / % possible all: 81.2

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (6-FEB-2020)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BKG

7bkg


Resolution: 2.691→41.97 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.804 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.484
RfactorNum. reflection% reflectionSelection details
Rfree0.3144 1317 -RANDOM
Rwork0.2088 ---
obs0.2141 26310 88 %-
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1--4.8617 Å2-3.5181 Å2-0.1083 Å2
2--5.2033 Å20.1549 Å2
3----0.3416 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.691→41.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8104 0 140 265 8509
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088437HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0611444HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2918SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1380HARMONIC5
X-RAY DIFFRACTIONt_it8437HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1060SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6943SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion21.85
LS refinement shellResolution: 2.691→2.72 Å
RfactorNum. reflection% reflection
Rfree0.3247 17 -
Rwork0.2816 --
obs--53.16 %

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