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- PDB-9atv: X-ray co-crystal structure of NCGC00685960 / NCATS-SM9335 in NNMT -

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Basic information

Entry
Database: PDB / ID: 9atv
TitleX-ray co-crystal structure of NCGC00685960 / NCATS-SM9335 in NNMT
ComponentsNicotinamide N-methyltransferase
KeywordsTRANSFERASE / NNMT / inhibitor / tumor
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.413 Å
AuthorsOlland, A. / White, A. / Suto, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nature / Year: 2025
Title: NNMT inhibition in cancer-associated fibroblasts restores antitumour immunity.
Authors: Heide, J. / Bilecz, A.J. / Patnaik, S. / Allega, M.F. / Donle, L. / Yang, K. / Teich, E. / Li, Y. / Lin, Q. / Kong, K. / Liu, L. / Yang, T.G. / Cheng, K.C. / Shrimp, J.H. / Hanson, Q.M. / ...Authors: Heide, J. / Bilecz, A.J. / Patnaik, S. / Allega, M.F. / Donle, L. / Yang, K. / Teich, E. / Li, Y. / Lin, Q. / Kong, K. / Liu, L. / Yang, T.G. / Cheng, K.C. / Shrimp, J.H. / Hanson, Q.M. / Shen, M. / Sun, H. / Shah, H. / Schweizer, L. / Zawieracz, K. / Olland, A. / White, A. / Suto, R.K. / Alhunayan, R. / Tasdemir, M. / Longman, N. / Liang, H. / Mann, M. / Stott, G.M. / Hall, M.D. / Schworer, S. / Weichselbaum, R.R. / Piffko, A. / Lengyel, E.
History
DepositionFeb 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 8, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,6636
Polymers94,3983
Non-polymers1,2653
Water1,71195
1
A: Nicotinamide N-methyltransferase
hetero molecules

C: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7754
Polymers62,9322
Non-polymers8432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-y,x-y+1,z-1/31
Buried area2280 Å2
ΔGint-9 kcal/mol
Surface area22110 Å2
MethodPISA
2
B: Nicotinamide N-methyltransferase
hetero molecules

B: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7754
Polymers62,9322
Non-polymers8432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area2200 Å2
ΔGint-9 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.596, 91.596, 213.257
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-428-

HOH

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Components

#1: Protein Nicotinamide N-methyltransferase


Mass: 31466.033 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P40261, nicotinamide N-methyltransferase
#2: Chemical ChemComp-A1AF6 / (8M)-8-{3-[(3S)-1-(2-cyclohexylethyl)piperidin-3-yl]-5-oxo-4,5-dihydro-1H-1,2,4-triazol-1-yl}quinolin-2(1H)-one


Mass: 421.535 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H31N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.74 Å3/Da / Density % sol: 55.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.15 M DL-Malic acid pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.41→50 Å / Num. obs: 40333 / % possible obs: 99 % / Redundancy: 5.4 % / CC1/2: 0.999 / Net I/σ(I): 16.3
Reflection shellResolution: 2.41→2.5 Å / Num. unique obs: 4150 / CC1/2: 0.939 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.82)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.413→45.798 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.177 / SU B: 24.628 / SU ML: 0.241 / Average fsc free: 0.9445 / Average fsc work: 0.9517 / Cross valid method: FREE R-VALUE / ESU R: 0.342 / ESU R Free: 0.235
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2343 1922 4.771 %
Rwork0.1965 38365 -
all0.198 --
obs-40287 98.912 %
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: 70.917 Å2
Baniso -1Baniso -2Baniso -3
1--0.107 Å2-0.054 Å2-0 Å2
2---0.107 Å2-0 Å2
3---0.348 Å2
Refinement stepCycle: LAST / Resolution: 2.413→45.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6197 0 93 95 6385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0126447
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166141
X-RAY DIFFRACTIONr_angle_refined_deg1.081.858735
X-RAY DIFFRACTIONr_angle_other_deg0.3451.76714245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885798
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.205526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.789101121
X-RAY DIFFRACTIONr_dihedral_angle_6_deg10.66410260
X-RAY DIFFRACTIONr_chiral_restr0.0450.2970
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021389
X-RAY DIFFRACTIONr_nbd_refined0.1920.21146
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.25190
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23066
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.23221
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2172
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0420.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1530.223
X-RAY DIFFRACTIONr_nbd_other0.1460.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0810.211
X-RAY DIFFRACTIONr_mcbond_it1.1395.353183
X-RAY DIFFRACTIONr_mcbond_other1.1385.353183
X-RAY DIFFRACTIONr_mcangle_it1.9679.6233975
X-RAY DIFFRACTIONr_mcangle_other1.9669.6243976
X-RAY DIFFRACTIONr_scbond_it1.2555.4713264
X-RAY DIFFRACTIONr_scbond_other1.2555.4713265
X-RAY DIFFRACTIONr_scangle_it2.17410.0354757
X-RAY DIFFRACTIONr_scangle_other2.17410.0354758
X-RAY DIFFRACTIONr_lrange_it3.57150.6586939
X-RAY DIFFRACTIONr_lrange_other3.56150.6476930
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.413-2.4760.3841150.38628090.38629540.8890.87198.98440.317
2.476-2.5430.3991160.38127280.38228740.8380.86398.95620.315
2.543-2.6170.3171170.30626740.30727950.9260.93199.85690.257
2.617-2.6970.3431250.31225910.31327370.9220.93299.23270.26
2.697-2.7850.3091440.27524990.27726510.9390.95199.69820.238
2.785-2.8830.2981050.27224410.27325550.9470.95599.64780.239
2.883-2.9910.279920.24523850.24624860.9480.96599.6380.21
2.991-3.1130.2911210.23522390.23823700.9530.96799.57810.206
3.113-3.250.2881140.21821780.22223160.9550.9798.96370.197
3.25-3.4080.2631620.21420290.21722080.9540.97199.23010.19
3.408-3.5910.241950.19319550.19620870.9670.97698.22710.172
3.591-3.8080.2421210.18318540.18719990.9650.97998.79940.169
3.808-4.0690.221940.17217480.17518710.9720.98198.450.162
4.069-4.3920.203750.1616660.16217640.9750.98598.69610.152
4.392-4.8060.189680.13915370.14116230.9820.98898.89090.134
4.806-5.3660.205670.15213920.15514820.9710.98798.4480.15
5.366-6.1820.198570.17712330.17813190.9760.98397.80140.171
6.182-7.5380.212450.17410780.17511490.9750.98497.73720.172
7.538-10.5180.168640.1298100.1329050.9790.9996.57460.137
10.518-45.7980.192250.2195190.2175710.9850.97195.27150.239
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.21170.6672-0.41251.915-0.17873.01490.0809-0.0431-0.0254-0.0446-0.0744-0.0217-0.04130.0186-0.00640.03070.0358-0.0130.0527-0.01710.007-51.297518.9907-39.4517
22.48520.1278-0.52022.08010.09123.38820.0764-0.04-0.1370.1084-0.0671-0.1175-0.04370.2271-0.00930.1392-0.0996-0.0350.14210.02760.0193-87.8744-9.0743-18.1928
31.47110.64670.07442.00250.62223.57710.04-0.0140.0048-0.0872-0.0475-0.00330.1616-0.07380.00750.0710.0207-0.01470.1292-0.02530.032-51.609219.73-4.7063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA3 - 301
2X-RAY DIFFRACTION2ALLB2 - 301
3X-RAY DIFFRACTION3ALLC1 - 301

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