MiMeDB: Showing metabocard for Deoxynojirimycin (MMDBc0004795)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-14 22:38:14 UTC

Update Date

2022-08-31 06:22:59 UTC

Metabolite ID

MMDBc0004795

Metabolite Identification

Common Name

Deoxynojirimycin

Description

Duvoglustat, also known as moranolin or bay-H-5595, 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. Duvoglustat is a very strong basic compound (based on its pKa). An optically active form of 2-(hydroxymethyl)piperidine-3,4,5-triol having 2R,3R,4R,5S-configuration.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05041402522D          

 15 15  0  0  1  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  2  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  2  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
    0.1842   -1.0445    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2822   -0.7752    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  6  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
  4  9  1  1  0  0  0
  5 10  1  1  0  0  0
  6 11  1  6  0  0  0
  3 12  1  1  0  0  0
  4 13  1  6  0  0  0
  5 14  1  6  0  0  0
  6 15  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0004795

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(O)CN[C@]([H])(CO)[C@@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C6H13NO4/c8-2-3-5(10)6(11)4(9)1-7-3/h3-11H,1-2H2/t3-,4+,5-,6-/m1/s1

> <INCHI_KEY>
LXBIFEVIBLOUGU-JGWLITMVSA-N

> <FORMULA>
C6H13NO4

> <MOLECULAR_WEIGHT>
163.1717

> <EXACT_MASS>
163.084457909

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
15.847626568631387

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   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   0.000   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    4    7                                                       
CONECT    2    3    8                                                       
CONECT    3    2    5    7   12                                             
CONECT    4    1    6    9   13                                             
CONECT    5    3    6   10   14                                             
CONECT    6    4    5   11   15                                             
CONECT    7    1    3                                                       
CONECT    8    2                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    6                                                            
CONECT   12    3                                                            
CONECT   13    4                                                            
CONECT   14    5                                                            
CONECT   15    6                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

Synonyms

Value	Source
(+)-1-Deoxynojirimycin	ChEBI
1,5-Deoxy-1,5-imino-D-mannitol	ChEBI
1,5-Dideoxy-1,5-imino-D-glucitol	ChEBI
1-Deoxymannojirimycin	ChEBI
1-Deoxynojirimycin	ChEBI
5-Amino-1,5-dideoxy-D-glucopyranose	ChEBI
BAY-H-5595	ChEBI
D-1-Deoxynojirimycin	ChEBI
DNJ	ChEBI
Moranolin	ChEBI
Moranoline	ChEBI
1 Deoxymannojirimycin	MeSH
1,5-Dideoxy-1,5-imino-D-mannitol	MeSH
1-Deoxynojirimycin hydrochloride	MeSH
1 Deoxynojirimycin	MeSH
1 Deoxynojirimycin hydrochloride	MeSH
Bay N 5595	MeSH

Molecular Formula

C₆H₁₃NO₄

Average Mass

163.1717

Monoisotopic Mass

163.084457909

IUPAC Name

(2R,3R,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol

Traditional Name

(2R,3R,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol

CAS Registry Number

Not Available

SMILES

[H][C@]1(O)CN[C@]([H])(CO)[C@@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C6H13NO4/c8-2-3-5(10)6(11)4(9)1-7-3/h3-11H,1-2H2/t3-,4+,5-,6-/m1/s1

InChI Key

LXBIFEVIBLOUGU-JGWLITMVSA-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.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Piperidines

Sub Class

Not Available

Direct Parent

Piperidines

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 Framework

Aliphatic heteromonocyclic compounds

External Descriptors

2-(hydroxymethyl)piperidine-3,4,5-triol (CHEBI:44369 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	511 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-2.9	ChemAxon
logS	0.5	ALOGPS
pKa (Strongest Acidic)	12.91	ChemAxon
pKa (Strongest Basic)	8.06	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	92.95 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	36.57 m³·mol⁻¹	ChemAxon
Polarizability	15.85 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0feb-7900000000-536465f5fd772045b134	2017-08-28	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01ot-0900000000-1aa3b43d5d62c90ccec7	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-002b-1900000000-6ef4261b9d4ed14a1746	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-056r-9500000000-2fa2710d2d9b3ef5535d	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-0900000000-38feb13cf90cc926e8b8	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03ec-1900000000-037cddc0c0bea31e7736	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-006x-9100000000-906240cbc58537e93cbd	2017-07-26	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	1	Human	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

DB03206

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00029420

Chemspider ID

Not Available

KEGG Compound ID

C16843

BioCyc ID

1-DEOXYNOJIRIMYCIN

BiGG ID

Not Available

Wikipedia Link

1-Deoxynojirimycin

METLIN ID

Not Available

PubChem Compound

29435

PDB ID

Not Available

ChEBI ID

44369

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Deoxynojirimycin (MMDBc0004795)

MOL for #<Metabolite:0x00007fecf8a18898>

3D MOL for #<Metabolite:0x00007fecf8a18898>

3D SDF for #<Metabolite:0x00007fecf8a18898>

3D-SDF for #<Metabolite:0x00007fecf8a18898>

PDB for #<Metabolite:0x00007fecf8a18898>

3D PDB for #<Metabolite:0x00007fecf8a18898>

SMILES for #<Metabolite:0x00007fecf8a18898>

INCHI for #<Metabolite:0x00007fecf8a18898>

Structure for #<Metabolite:0x00007fecf8a18898>

3D Structure for #<Metabolite:0x00007fecf8a18898>