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- PDB-7wmt: Crystal structure of small molecule 13 bound to human Nicotinamid... -

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Basic information

Entry
Database: PDB / ID: 7wmt
TitleCrystal structure of small molecule 13 bound to human Nicotinamide N-methyltransferase
ComponentsNicotinamide N-methyltransferase
KeywordsTRANSFERASE / Nicotinamide N-methyltransferase
Function / homology
Function and homology information


pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / positive regulation of protein deacetylation / NAD biosynthesis via nicotinamide riboside salvage pathway / Methylation / Nicotinamide salvaging / animal organ regeneration ...pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / positive regulation of protein deacetylation / NAD biosynthesis via nicotinamide riboside salvage pathway / Methylation / Nicotinamide salvaging / animal organ regeneration / positive regulation of gluconeogenesis / response to organonitrogen compound / 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-1IV / Nicotinamide N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 Å
AuthorsYoshida, S. / Uehara, S. / Kondo, N. / Takahashi, Y. / Yamamoto, S. / Kameda, A. / Kawagoe, S. / Inoue, N. / Yamada, M. / Yoshimura, N. / Tachibana, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides.
Authors: Yoshida, S. / Uehara, S. / Kondo, N. / Takahashi, Y. / Yamamoto, S. / Kameda, A. / Kawagoe, S. / Inoue, N. / Yamada, M. / Yoshimura, N. / Tachibana, Y.
History
DepositionJan 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2482
Polymers27,6841
Non-polymers5641
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.654, 62.654, 67.121
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Nicotinamide N-methyltransferase


Mass: 27683.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT / Production host: Escherichia coli (E. coli)
References: UniProt: P40261, nicotinamide N-methyltransferase
#2: Chemical ChemComp-1IV / [(2~{R},4~{S})-4-[2-(aminomethyl)imidazol-1-yl]-2-[1-[(4-chlorophenyl)methyl]-5-methyl-indol-2-yl]pyrrolidin-1-yl]-(1~{H}-pyrrolo[2,3-b]pyridin-5-yl)methanone


Mass: 564.080 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H30ClN7O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.04 M Potassium phosphate monobasic, 16 % w/v PEG 8000, 20 % v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.77→54.26 Å / Num. obs: 28583 / % possible obs: 99.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.017 / Rrim(I) all: 0.04 / Χ2: 1.082 / Net I/σ(I): 28.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.77-1.834.80.24727090.9460.1260.2781.01394.3
1.83-1.914.90.1728810.9770.0860.1911.066100
1.91-1.994.90.1228880.9860.060.1351.155100
1.99-2.14.90.08928740.9920.0440.11.134100
2.1-2.2350.07228550.9950.0360.0811.167100
2.23-2.450.05628870.9960.0280.0631.111100
2.4-2.645.10.04828500.9970.0240.0541.09100
2.64-3.035.10.0428950.9980.0190.0441.037100
3.03-3.815.20.03128660.9990.0150.0351.131100
3.81-505.20.02728780.9990.0130.030.91899.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.35
Highest resolutionLowest resolution
Rotation28.54 Å2.07 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0218refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREP11.6.02phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→54.26 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.927 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0926 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1909 1405 4.9 %RANDOM
Rwork0.1548 ---
obs0.1567 27157 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 114.48 Å2 / Biso mean: 43.953 Å2 / Biso min: 22.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å2-0 Å2
2---0.03 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 1.77→54.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1777 0 41 202 2020
Biso mean--34.73 54.76 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021894
X-RAY DIFFRACTIONr_angle_refined_deg2.1222.022580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3135236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53825.25678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00415328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.132157
X-RAY DIFFRACTIONr_chiral_restr0.1580.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211417
LS refinement shellResolution: 1.772→1.818 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 106 -
Rwork0.174 1948 -
all-2054 -
obs--97.67 %

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