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Showing NP-Card for 1-Deoxynojirimycin (NP0137042)

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Record Information
Version2.0
Created at2022-05-30 16:39:55 UTC
Updated at2022-05-30 16:39:55 UTC
NP-MRD IDNP0137042
Secondary Accession NumbersNone
Natural Product Identification
Common Name1-Deoxynojirimycin
Description1-Deoxynojirimycin, also known as antibiotic S-gi or 1HXK, belongs to the class of organic compounds known as piperidines. Piperidines are compounds containing a piperidine ring, which is a saturated aliphatic six-member ring with one nitrogen atom and five carbon atoms. 1-Deoxynojirimycin (DNJ or 1-DNJ), also called duvoglustat or moranolin, is an alpha-glucosidase inhibitor, most commonly found in mulberry leaves. 1-Deoxynojirimycin is a very strong basic compound (based on its pKa). Outside of the human body, 1-Deoxynojirimycin has been detected, but not quantified in, fruits. This could make 1-deoxynojirimycin a potential biomarker for the consumption of these foods. This results in the product 1-DNJ.In the Streptomyces subrutilus species, a secondary pathway branching from the manojirimycin precursor results in 1-deoxymanojirimycin via dehydration and reduction of the isomer. GabT1 catalyzes transamination at the C2 position, followed by a dephosphorylation by the Yktc1 enzyme, resulting in 2-amino-2-deoxy-D-mannitol (ADM), an essential precursor. Nojirimycin is then dehydrated (loss of -OH at C1 position), along with reduction of the imine moiety. Azasugar biosynthesis in Commelina communis involves C1-C5 cyclisation of the original D-glucose precursor without the subsequent inversion. Although it can be obtained in small quantities by brewing an herbal tea from mulberry leaves, interest in commercial production has led to research on developing mulberry tea higher in DNJ, and on alternate routes of production, such as via Bacillus species.1-Deoxynojirimycin is a polyhydroxylated piperidine alkaloid produced from D-Glucose in various plants, such as Commelina communis, and in the Streptomyces and Bacillus bacteria. Regio-selective oxidation by GutB1 occurs at the exposed C6 hydroxyl of ADM, pushing a C2-N-C6 cyclization of the resulting 6-oxo intermediate, creating Manojirimycin (MJ). 1-Deoxynojirimycin is found in Adenophora triphylla, Alrawia bellii, Angylocalyx pynaertii, Bombyx mori, Commelina communis, Dorstenia psilurus, Hyacinthus orientalis, Lonchocarpus heptaphyllus, Lonchocarpus sericeus, Morus alba, Morus australis, Morus bombycis, Omphalea diandra, Parmotrema praesorediosum, Scilla siberica, Streptomyces lavendulae and Streptomyces subrutilus. High quantities of this azasugar are produced in Bacillus subtilis, a process initiated by a TYB gene cluster composed of gabT1 (aminotransferase), yktc1 (phosphatase), and gutB1 (oxidoreductase).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0137042 (1-Deoxynojirimycin)


  Mrv0541 05061308242D          

 11 11  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  1  1  0  0  0  0
  7  3  1  0  0  0  0
  8  2  1  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  6  1  0  0  0  0
M  END
Download

3D MOL for NP0137042 (1-Deoxynojirimycin)

     RDKit          3D

 24 24  0  0  0  0  0  0  0  0999 V2000
    3.1025    0.8266   -0.0439 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3329   -0.1120   -0.7252 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0224   -0.3987    0.0165 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3142   -1.3649   -0.7590 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8912   -1.7263   -0.0441 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7902   -0.5399   -0.0908 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.9503   -0.8671    0.6476 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1974    0.7246    0.4200 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8432    1.7838   -0.2647 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2683    0.8513    0.3077 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5715    1.8535   -0.6391 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4536    0.4660    0.8084 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9303   -1.0485   -0.7532 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1483    0.2646   -1.7465 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3370   -0.8942    0.9736 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9020   -2.2198   -0.8286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7013   -1.9740    1.0198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3730   -2.5494   -0.6023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1680   -0.4057   -1.1466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5497   -0.0801    0.6345 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5463    0.8454    1.4885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8443    2.6087    0.2538 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6626    1.2510    1.2891 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8095    2.7052   -0.2155 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10  3  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  1
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  6
  7 20  1  0
  8 21  1  1
  9 22  1  0
 10 23  1  1
 11 24  1  0
M  END
Download

3D SDF for NP0137042 (1-Deoxynojirimycin)


  Mrv0541 05061308242D          

 11 11  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  1  1  0  0  0  0
  7  3  1  0  0  0  0
  8  2  1  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  6  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0137042

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1NCC(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H13NO4/c8-2-3-5(10)6(11)4(9)1-7-3/h3-11H,1-2H2

> <INCHI_KEY>
LXBIFEVIBLOUGU-UHFFFAOYSA-N

> <FORMULA>
C6H13NO4

> <MOLECULAR_WEIGHT>
163.1717

> <EXACT_MASS>
163.084457909

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
15.849220843979085

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(hydroxymethyl)piperidine-3,4,5-triol

> <ALOGPS_LOGP>
-2.22

> <JCHEM_LOGP>
-2.885743183

> <ALOGPS_LOGS>
0.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.040882857401087

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.906053630987142

> <JCHEM_PKA_STRONGEST_BASIC>
8.062727249499266

> <JCHEM_POLAR_SURFACE_AREA>
92.95

> <JCHEM_REFRACTIVITY>
36.5744

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.11e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1 deoxynojirimycin

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0137042 (1-Deoxynojirimycin)

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PDB for NP0137042 (1-Deoxynojirimycin)
HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    4    7                                                       
CONECT    2    3    8                                                       
CONECT    3    2    5    7                                                  
CONECT    4    1    6    9                                                  
CONECT    5    3    6   10                                                  
CONECT    6    4    5   11                                                  
CONECT    7    1    3                                                       
CONECT    8    2                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    6                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for NP0137042 (1-Deoxynojirimycin)
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SMILES for NP0137042 (1-Deoxynojirimycin)
OCC1NCC(O)C(O)C1O
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INCHI for NP0137042 (1-Deoxynojirimycin)
InChI=1S/C6H13NO4/c8-2-3-5(10)6(11)4(9)1-7-3/h3-11H,1-2H2
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Synonyms
ValueSource
(2R,3R,4R,5S)-2-(Hydroxymethyl)piperidine-3,4,5-triolHMDB
1,5-Dideoxy-1,5-imino-D-glucitol, 9ciHMDB
1-DEOXY-nojirimycinHMDB
1-DeoxymannojirimycinHMDB
1-Deoxynojirimycin (DNJ)HMDB
1HXKHMDB
1OimHMDB
Antibiotic S-giHMDB
MoranolineHMDB
NOJHMDB
S-GIHMDB
1,5-Dideoxy-1,5-imino-D-mannitolMeSH
1-Deoxynojirimycin hydrochlorideMeSH
1 DeoxynojirimycinMeSH
1,5-Deoxy-1,5-imino-D-mannitolMeSH
Bay N 5595MeSH
1 DeoxymannojirimycinMeSH
1-DeoxynojirimycinMeSH
1 Deoxynojirimycin hydrochlorideMeSH
Chemical FormulaC6H13NO4
Average Mass163.1717 Da
Monoisotopic Mass163.08446 Da
IUPAC Name2-(hydroxymethyl)piperidine-3,4,5-triol
Traditional Name1 deoxynojirimycin
CAS Registry NumberNot Available
SMILES
OCC1NCC(O)C(O)C1O
InChI Identifier
InChI=1S/C6H13NO4/c8-2-3-5(10)6(11)4(9)1-7-3/h3-11H,1-2H2
InChI KeyLXBIFEVIBLOUGU-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Adenophora triphyllaLOTUS Database
Alrawia belliiLOTUS Database
Angylocalyx pynaertiiLOTUS Database
Bombyx moriLOTUS Database
Commelina communisLOTUS Database
Dorstenia psilurusLOTUS Database
Hyacinthus orientalisLOTUS Database
Lonchocarpus latifoliusLOTUS Database
Lonchocarpus sericeusLOTUS Database
Morus albaLOTUS Database
Morus australisLOTUS Database
Morus bombycisLOTUS Database
Omphalea diandraLOTUS Database
Parmotrema praesorediosumLOTUS Database
Scilla sibericaLOTUS Database
Streptomyces lavendulaeLOTUS Database
Streptomyces subrutilusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as piperidines. Piperidines are compounds containing a piperidine ring, which is a saturated aliphatic six-member ring with one nitrogen atom and five carbon atoms.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPiperidines  
Sub ClassNot Available
Direct ParentPiperidines  
Alternative Parents
Substituents
  • Piperidine
    • 

  • 1,2-aminoalcohol
    • 

  • Secondary alcohol
    • 

  • Secondary aliphatic amine
    • 

  • Polyol
    • 

  • Secondary amine
    • 

  • Azacycle
    • 

  • Primary alcohol
    • 

  • Alcohol
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic nitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Amine
    • 

  • Hydrocarbon derivative
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.2ALOGPS
logP-2.9ChemAxon
logS0.5ALOGPS
pKa (Strongest Acidic)12.91ChemAxon
pKa (Strongest Basic)8.06ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area92.95 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity36.57 m³·mol⁻¹ChemAxon
Polarizability15.85 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0035359  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB014031  
KNApSAcK IDC00029420  
Chemspider ID1333  
KEGG Compound IDC16843  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link1-Deoxynojirimycin  
METLIN IDNot Available
PubChem Compound1374  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available