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Showing metabocard for 1-Deoxynojirimycin (HMDB0035359)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 20:20:05 UTC
Update Date2022-09-22 18:34:26 UTC
HMDB IDHMDB0035359
Secondary Accession Numbers
  • HMDB35359
Metabolite Identification
Common Name1-Deoxynojirimycin
Description1-Deoxynojirimycin 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 has been detected, but not quantified in, fruits. This could make 1-deoxynojirimycin a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 1-Deoxynojirimycin.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0035359 (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
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3D MOL for HMDB0035359 (1-Deoxynojirimycin)

HMDB0251008
     RDKit          3D
1-Deoxymannojirimycin
 24 24  0  0  0  0  0  0  0  0999 V2000
    3.2900   -0.8802   -0.1392 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4323    0.1052   -0.6237 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1007   -0.0339    0.0492 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4925   -1.3286   -0.1960 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6825   -1.5349    0.5630 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6092   -0.3783    0.6778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6514   -0.4275   -0.2722 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9936    0.9682    0.6020 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9823    1.9190    0.3230 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0931    0.9813   -0.4499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4888    0.4599   -1.6233 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6137   -0.6727    0.7725 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3847    0.0964   -1.7178 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8741    1.0778   -0.3255 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2653    0.0614    1.1428 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3586   -1.4156   -1.2313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2424   -2.3912    0.1050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3881   -1.9132    1.5843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1189   -0.4529    1.6782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4742   -1.0833   -0.9735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5028    1.2940    1.5552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0027    2.6516    0.9892 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5393    1.9622   -0.6135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3074    0.9353   -1.8762 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  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
  7 20  1  0
  8 21  1  0
  9 22  1  0
 10 23  1  0
 11 24  1  0
M  END
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3D SDF for HMDB0035359 (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>
HMDB0035359

> <DATABASE_NAME>
hmdb

> <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

$$$$
Download

3D-SDF for HMDB0035359 (1-Deoxynojirimycin)

HMDB0251008
     RDKit          3D
1-Deoxymannojirimycin
 24 24  0  0  0  0  0  0  0  0999 V2000
    3.2900   -0.8802   -0.1392 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4323    0.1052   -0.6237 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1007   -0.0339    0.0492 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4925   -1.3286   -0.1960 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6825   -1.5349    0.5630 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6092   -0.3783    0.6778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6514   -0.4275   -0.2722 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9936    0.9682    0.6020 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9823    1.9190    0.3230 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0931    0.9813   -0.4499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4888    0.4599   -1.6233 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6137   -0.6727    0.7725 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3847    0.0964   -1.7178 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8741    1.0778   -0.3255 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2653    0.0614    1.1428 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3586   -1.4156   -1.2313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2424   -2.3912    0.1050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3881   -1.9132    1.5843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1189   -0.4529    1.6782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4742   -1.0833   -0.9735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5028    1.2940    1.5552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0027    2.6516    0.9892 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5393    1.9622   -0.6135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3074    0.9353   -1.8762 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  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
  7 20  1  0
  8 21  1  0
  9 22  1  0
 10 23  1  0
 11 24  1  0
M  END
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PDB for HMDB0035359 (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 HMDB0035359 (1-Deoxynojirimycin)

COMPND    HMDB0249990
HETATM    1  O1  UNL     1       3.262  -0.310   0.462  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.235   0.496   0.004  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.918   0.114   0.704  1.00  0.00           C  
HETATM    4  N1  UNL     1       0.675  -1.236   0.385  1.00  0.00           N  
HETATM    5  C3  UNL     1      -0.433  -1.544  -0.419  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.663  -0.859   0.128  1.00  0.00           C  
HETATM    7  O2  UNL     1      -2.770  -1.248  -0.609  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.498   0.625   0.164  1.00  0.00           C  
HETATM    9  O3  UNL     1      -2.003   1.121  -1.062  1.00  0.00           O  
HETATM   10  C6  UNL     1      -0.124   1.105   0.421  1.00  0.00           C  
HETATM   11  O4  UNL     1       0.289   1.883  -0.686  1.00  0.00           O  
HETATM   12  H1  UNL     1       3.828   0.166   1.122  1.00  0.00           H  
HETATM   13  H2  UNL     1       2.396   1.571   0.189  1.00  0.00           H  
HETATM   14  H3  UNL     1       2.036   0.356  -1.076  1.00  0.00           H  
HETATM   15  H4  UNL     1       1.200   0.153   1.797  1.00  0.00           H  
HETATM   16  H5  UNL     1       0.947  -1.935   1.100  1.00  0.00           H  
HETATM   17  H6  UNL     1      -0.285  -1.314  -1.513  1.00  0.00           H  
HETATM   18  H7  UNL     1      -0.625  -2.639  -0.368  1.00  0.00           H  
HETATM   19  H8  UNL     1      -1.804  -1.234   1.161  1.00  0.00           H  
HETATM   20  H9  UNL     1      -2.466  -1.683  -1.452  1.00  0.00           H  
HETATM   21  H10 UNL     1      -2.242   1.011   0.925  1.00  0.00           H  
HETATM   22  H11 UNL     1      -1.795   2.095  -1.106  1.00  0.00           H  
HETATM   23  H12 UNL     1      -0.179   1.855   1.267  1.00  0.00           H  
HETATM   24  H13 UNL     1       0.102   1.452  -1.536  1.00  0.00           H  
CONECT    1    2   12
CONECT    2    3   13   14
CONECT    3    4   10   15
CONECT    4    5   16
CONECT    5    6   17   18
CONECT    6    7    8   19
CONECT    7   20
CONECT    8    9   10   21
CONECT    9   22
CONECT   10   11   23
CONECT   11   24
END
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SMILES for HMDB0035359 (1-Deoxynojirimycin)

OCC1NCC(O)C(O)C1O
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INCHI for HMDB0035359 (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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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H13NO4
Average Molecular Weight163.1717
Monoisotopic Molecular Weight163.084457909
IUPAC Name2-(hydroxymethyl)piperidine-3,4,5-triol
Traditional Name1 deoxynojirimycin
CAS Registry Number19130-96-2
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
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
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Industrial applicationBiological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point206 °CNot Available
Boiling Point361.12 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-1.80Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB 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
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1666961
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Enzymes

Enzyme Details
1. Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
General function:
Involved in mannosyl-oligosaccharide 1,2-alpha-mannosidase activity
Specific function:
Involved in glycoprotein quality control targeting of misfolded glycoproteins for degradation. It primarily trims a single alpha-1,2-linked mannose residue from Man(9)GlcNAc(2) to produce Man(8)GlcNAc(2), but at high enzyme concentrations, as found in the ER quality control compartment (ERQC), it further trims the carbohydrates to Man(5-6)GlcNAc(2).
Gene Name:
MAN1B1
Uniprot ID:
Q9UKM7
Molecular weight:
79579.18
References
  1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235 ]