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Yorodumi- PDB-7eu5: Co-crystal structure of Human Nicotinamide N-methyltransferase (N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7eu5 | ||||||
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Title | Co-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with tricyclic small molecule inhibitor JBSNF-000107 | ||||||
Components | Nicotinamide N-methyltransferase | ||||||
Keywords | TRANSFERASE / NNMT | ||||||
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 / NAD biosynthesis via nicotinamide riboside salvage pathway / positive regulation of protein deacetylation / Methylation / Nicotinamide salvaging / : ...pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / NAD biosynthesis via nicotinamide riboside salvage pathway / positive regulation of protein deacetylation / Methylation / Nicotinamide salvaging / : / animal organ regeneration / positive regulation of gluconeogenesis / methylation / response to xenobiotic stimulus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.731 Å | ||||||
Authors | Swaminathan, S. / Gosu, R. / Birudukota, S. / Kandan, S. / Vaithilingam, K. | ||||||
Citation | Journal: Sci Rep / Year: 2022 Title: Novel tricyclic small molecule inhibitors of Nicotinamide N-methyltransferase for the treatment of metabolic disorders. Authors: Ruf, S. / Rajagopal, S. / Kadnur, S.V. / Hallur, M.S. / Rani, S. / Kristam, R. / Swaminathan, S. / Zope, B.R. / Gondrala, P.K. / Swamy, I. / Putta, V.P.R.K. / Kandan, S. / Zech, G. / ...Authors: Ruf, S. / Rajagopal, S. / Kadnur, S.V. / Hallur, M.S. / Rani, S. / Kristam, R. / Swaminathan, S. / Zope, B.R. / Gondrala, P.K. / Swamy, I. / Putta, V.P.R.K. / Kandan, S. / Zech, G. / Schreuder, H. / Rudolph, C. / Elvert, R. / Czech, J. / Birudukota, S. / Siddiqui, M.A. / Anand, N.N. / Mane, V.S. / Dittakavi, S. / Suresh, J. / Gosu, R. / Ramesh, M. / Yura, T. / Dhakshinamoorthy, S. / Kannt, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eu5.cif.gz | 215.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eu5.ent.gz | 164.6 KB | Display | PDB format |
PDBx/mmJSON format | 7eu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eu5_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 7eu5_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 7eu5_validation.xml.gz | 39.1 KB | Display | |
Data in CIF | 7eu5_validation.cif.gz | 52.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/7eu5 ftp://data.pdbj.org/pub/pdb/validation_reports/eu/7eu5 | HTTPS FTP |
-Related structure data
Related structure data | 7et7C 3rodS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 31236.717 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 (E. coli) References: UniProt: P40261, nicotinamide N-methyltransferase #2: Chemical | ChemComp-SAH / #3: Chemical | ChemComp-JDL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.07 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.2, 24 %(w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→48.73 Å / Num. obs: 25314 / % possible obs: 94.6 % / Redundancy: 1.9 % / CC1/2: 0.923 / Rmerge(I) obs: 0.19 / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 2.71→2.84 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 1 / Num. unique obs: 2674 / CC1/2: 0.486 / % possible all: 74.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ROD Resolution: 2.731→48.73 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.837 / SU B: 25.222 / SU ML: 0.48 / Cross valid method: FREE R-VALUE / ESU R Free: 0.463 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||
Displacement parameters | Biso mean: 30.051 Å2
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Refinement step | Cycle: LAST / Resolution: 2.731→48.73 Å
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Refine LS restraints | Type: r_lrange_other / Dev ideal: 4.062 / Dev ideal target: 36.367 / Number: 8859 |