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Yorodumi- PDB-7wmt: Crystal structure of small molecule 13 bound to human Nicotinamid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wmt | ||||||
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Title | Crystal structure of small molecule 13 bound to human Nicotinamide N-methyltransferase | ||||||
Components | Nicotinamide N-methyltransferase | ||||||
Keywords | TRANSFERASE / 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 / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 Å | ||||||
Authors | Yoshida, S. / Uehara, S. / Kondo, N. / Takahashi, Y. / Yamamoto, S. / Kameda, A. / Kawagoe, S. / Inoue, N. / Yamada, M. / Yoshimura, N. / Tachibana, Y. | ||||||
Funding support | 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wmt.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wmt.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 7wmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wmt_validation.pdf.gz | 824.3 KB | Display | wwPDB validaton report |
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Full document | 7wmt_full_validation.pdf.gz | 830.2 KB | Display | |
Data in XML | 7wmt_validation.xml.gz | 14 KB | Display | |
Data in CIF | 7wmt_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/7wmt ftp://data.pdbj.org/pub/pdb/validation_reports/wm/7wmt | HTTPS FTP |
-Related structure data
Related structure data | 7wmcC 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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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-1IV / [( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.04 M Potassium phosphate monobasic, 16 % w/v PEG 8000, 20 % v/v Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 25, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.35
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-Processing
Software |
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Refinement | Method 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
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.48 Å2 / Biso mean: 43.953 Å2 / Biso min: 22.53 Å2
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Refinement step | Cycle: final / Resolution: 1.77→54.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.772→1.818 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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