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- PDB-21nj: Crystal structure of compound 10 bound to human Nicotinamide N-me... -

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Basic information

Entry
Database: PDB / ID: 21nj
TitleCrystal structure of compound 10 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 / positive regulation of protein deacetylation / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / nicotinamide metabolic process / nicotinate metabolic process / Methylation / NAD+ catabolic process / Nicotinate metabolism ...pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / positive regulation of protein deacetylation / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / nicotinamide metabolic process / nicotinate metabolic process / Methylation / NAD+ catabolic process / Nicotinate metabolism / positive regulation of gluconeogenesis / methylation / 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
: / Nicotinamide N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsYoshida, S. / Kondo, N. / Uehara, S. / Yoshimura, N. / Sako, Y. / Yamamoto, S. / Kitade, M. / Tachibana, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2026
Title: Structure-Based Drug Discovery of Non-SAM-Mimetic Bisubstrate Inhibitors against Nicotinamide N ‐Methyltransferase.
Authors: Yoshida, S. / Kondo, N. / Uehara, S. / Yoshimura, N. / Sako, Y. / Yamamoto, S. / Kitade, M. / Tachibana, Y.
History
DepositionDec 20, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3254
Polymers61,5602
Non-polymers7652
Water2,252125
1
A: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1632
Polymers30,7801
Non-polymers3821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-3 kcal/mol
Surface area10340 Å2
MethodPISA
2
B: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1632
Polymers30,7801
Non-polymers3821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-4 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.233, 73.690, 89.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nicotinamide N-methyltransferase


Mass: 30780.242 Da / Num. of mol.: 2
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-A1MDA / (3~{S})-~{N}-(2-oxidanylidene-3~{H}-1,3-benzothiazol-7-yl)-1-(2-pyridin-2-ylethyl)piperidine-3-carboxamide


Mass: 382.479 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N4O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
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: 1.91 Å3/Da / Density % sol: 35.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NaCl, 0.1 M imidazole pH7.26, 18%w/v PEG3350, 14%v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.26→56.95 Å / Num. obs: 22634 / % possible obs: 99.3 % / Redundancy: 4.7 % / Rpim(I) all: 0.07 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.26-2.344.70.40922280.8960.9720.2080.461.01499.2
2.34-2.434.70.35222370.9230.980.180.3970.99999.4
2.43-2.554.70.30222290.930.9820.1540.3411.02799.5
2.55-2.684.70.26822100.9390.9840.1360.3020.98299.5
2.68-2.854.70.22422550.9490.9870.1140.2520.97799.4
2.85-3.074.80.18122350.9660.9910.0920.2041.00399.2
3.07-3.384.70.14122590.9750.9940.0730.1590.96399.3
3.38-3.864.80.10622700.9810.9950.0550.120.96799.4
3.86-4.874.70.0923060.9880.9970.0470.1020.95299.4
4.87-104.50.07824050.9940.9990.0410.0891.04898.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→56.95 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.882 / SU B: 8.189 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.399 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26673 1189 5.3 %RANDOM
Rwork0.19219 ---
obs0.19602 21404 99.09 %-
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 mean: 26.899 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å20 Å2
2--0.08 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.26→56.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 54 125 4075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024057
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7152.0045513
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9155510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8125.443158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33815684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.635159
X-RAY DIFFRACTIONr_chiral_restr0.1070.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213015
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.8812.6182028
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8383.9152530
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5742.8152029
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.34822.196230
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.26→2.318 Å
RfactorNum. reflection% reflection
Rfree0.309 84 -
Rwork0.216 1525 -
obs--96.41 %

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