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- PDB-21nl: Crystal structure of compound 12 bound to human Nicotinamide N-me... -

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Basic information

Entry
Database: PDB / ID: 21nl
TitleCrystal structure of compound 12 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: 2.01 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)62,2774
Polymers61,5602
Non-polymers7172
Water4,774265
1
A: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1392
Polymers30,7801
Non-polymers3581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1392
Polymers30,7801
Non-polymers3581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.545, 73.294, 99.044
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-A1MDB / 3-[[[(1~{R},3~{S})-3-(1,3-thiazol-2-ylcarbamoyl)cyclohexyl]amino]methyl]benzamide


Mass: 358.458 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22N4O2S / 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
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: 1.9 Å3/Da / Density % sol: 35.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH8.0, 28%w/v PEG4000

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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: Mar 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.01→58.92 Å / Num. obs: 31957 / % possible obs: 99.7 % / Redundancy: 5.2 % / Rpim(I) all: 0.025 / Net I/σ(I): 16.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.01-2.0850.19431360.9680.9920.0940.2171.02599.7
2.08-2.175.20.16431460.9790.9950.0790.1831.12599.8
2.17-2.265.20.13931240.9840.9960.0670.1551.16299.7
2.26-2.385.30.11731850.990.9970.0560.131.04499.8
2.38-2.535.20.09431490.9920.9980.0440.1041.10499.9
2.53-2.735.30.07731870.9950.9990.0370.0861.09799.7
2.73-35.30.06531710.9960.9990.0311.07699.7
3-3.445.30.0532110.9970.9990.0231.0399.8
3.44-4.335.30.03832580.99810.0181.09999.7
4.33-105.10.02833900.99910.0130.99599.4

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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: 2.01→58.92 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.718 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24772 1593 5 %RANDOM
Rwork0.18332 ---
obs0.18651 30315 99.7 %-
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: 27.959 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.01→58.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3947 0 50 265 4262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.024097
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.9995565
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9125516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93624.937158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22815680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0571511
X-RAY DIFFRACTIONr_chiral_restr0.1260.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213059
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_it2.582.6792058
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3894.0032570
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.232.8952039
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.58423.2236513
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: 2.01→2.061 Å
RfactorNum. reflection% reflection
Rfree0.303 123 -
Rwork0.184 2176 -
obs--99.18 %

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