NP-MRD: Showing NP-Card for 1-deoxymannojirimycin (NP0013553)

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Record Information

Version

1.0

Created at

2021-01-05 22:52:46 UTC

Updated at

2021-07-15 17:14:47 UTC

NP-MRD ID

NP0013553

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1-deoxymannojirimycin

Provided By

NPAtlas

Description

1-Deoxymannojirimycin is also known as DMJ or bay N 5595. 1-deoxymannojirimycin is found in Adenophora triphylla, Agrobacterium, Angylocalyx pynaertii, Bacillus amyloliquefaciens, Bacillus polymyxa, Bacillus subtilis , Commelina communis, Commelina communis L , Morus bombycis , Morus spp., Murus sp., Omphalea queenslandiae and Streptomyces lavandulae subsp. trehalostaticus no.2882. It was first documented in 1989 (PMID: 2547743). Based on a literature review very few articles have been published on 1-deoxymannojirimycin.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242119373D          

 24 24  0  0  0  0            999 V2000
    2.8161   -0.0557    1.1680 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4098    0.0217   -0.1491 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9216   -0.0579   -0.3036 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3673   -1.2929    0.2103 N   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9079   -1.4610   -0.4095 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8172   -0.3055   -0.3472 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7727   -0.5317    0.6704 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2274    1.0271   -0.1465 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0121    1.7906    0.7495 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1780    1.0502    0.3634 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7442    2.2945    0.2138 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2190   -0.9443    1.3284 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7447    0.9591   -0.6386 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8443   -0.8255   -0.7338 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7045    0.0042   -1.4014 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9566   -2.1117    0.0473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3893   -2.3573    0.0815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7347   -1.7946   -1.4745 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4290   -0.2826   -1.2962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9931   -1.5101    0.5822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2388    1.6253   -1.0992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8293    1.5281    1.6894 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1318    0.8189    1.4609 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3136    2.4110   -0.5653 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10  3  1  0  0  0  0
  1 12  1  0  0  0  0
  2 13  1  0  0  0  0
  2 14  1  0  0  0  0
  3 15  1  6  0  0  0
  4 16  1  0  0  0  0
  5 17  1  0  0  0  0
  5 18  1  0  0  0  0
  6 19  1  6  0  0  0
  7 20  1  0  0  0  0
  8 21  1  6  0  0  0
  9 22  1  0  0  0  0
 10 23  1  1  0  0  0
 11 24  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0013553

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@@]1([H])N([H])C([H])([H])[C@@]([H])(O[H])[C@@]([H])(O[H])[C@]1([H])O[H]

> <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-KVTDHHQDSA-N

> <FORMULA>
C6H13NO4

> <MOLECULAR_WEIGHT>
163.1717

> <EXACT_MASS>
163.084457909

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
15.840167742216972

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R,5R)-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>
deoxymannojirimycin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  O   UNK     0       2.816  -0.056   1.168  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.410   0.022  -0.149  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.922  -0.058  -0.304  0.00  0.00           C+0
HETATM    4  N   UNK     0       0.367  -1.293   0.210  0.00  0.00           N+0
HETATM    5  C   UNK     0      -0.908  -1.461  -0.410  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.817  -0.306  -0.347  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.773  -0.532   0.670  0.00  0.00           O+0
HETATM    8  C   UNK     0      -1.227   1.027  -0.147  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.012   1.791   0.750  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.178   1.050   0.363  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.744   2.295   0.214  0.00  0.00           O+0
HETATM   12  H   UNK     0       3.219  -0.944   1.328  0.00  0.00           H+0
HETATM   13  H   UNK     0       2.745   0.959  -0.639  0.00  0.00           H+0
HETATM   14  H   UNK     0       2.844  -0.826  -0.734  0.00  0.00           H+0
HETATM   15  H   UNK     0       0.705   0.004  -1.401  0.00  0.00           H+0
HETATM   16  H   UNK     0       0.957  -2.112   0.047  0.00  0.00           H+0
HETATM   17  H   UNK     0      -1.389  -2.357   0.082  0.00  0.00           H+0
HETATM   18  H   UNK     0      -0.735  -1.795  -1.474  0.00  0.00           H+0
HETATM   19  H   UNK     0      -2.429  -0.283  -1.296  0.00  0.00           H+0
HETATM   20  H   UNK     0      -2.993  -1.510   0.582  0.00  0.00           H+0
HETATM   21  H   UNK     0      -1.239   1.625  -1.099  0.00  0.00           H+0
HETATM   22  H   UNK     0      -1.829   1.528   1.689  0.00  0.00           H+0
HETATM   23  H   UNK     0       0.132   0.819   1.461  0.00  0.00           H+0
HETATM   24  H   UNK     0       1.314   2.411  -0.565  0.00  0.00           H+0
CONECT    1    2   12                                                       
CONECT    2    1    3   13   14                                             
CONECT    3    2    4   10   15                                             
CONECT    4    3    5   16                                                  
CONECT    5    4    6   17   18                                             
CONECT    6    5    7    8   19                                             
CONECT    7    6   20                                                       
CONECT    8    6    9   10   21                                             
CONECT    9    8   22                                                       
CONECT   10    8   11    3   23                                             
CONECT   11   10   24                                                       
CONECT   12    1                                                            
CONECT   13    2                                                            
CONECT   14    2                                                            
CONECT   15    3                                                            
CONECT   16    4                                                            
CONECT   17    5                                                            
CONECT   18    5                                                            
CONECT   19    6                                                            
CONECT   20    7                                                            
CONECT   21    8                                                            
CONECT   22    9                                                            
CONECT   23   10                                                            
CONECT   24   11                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   48    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
DMJ	Kegg
1 Deoxymannojirimycin	MeSH
1 Deoxynojirimycin	MeSH
1 Deoxynojirimycin hydrochloride	MeSH
1,5-Deoxy-1,5-imino-D-mannitol	MeSH
1,5-Dideoxy-1,5-imino-D-mannitol	MeSH
1-Deoxynojirimycin	MeSH
1-Deoxynojirimycin hydrochloride	MeSH
Bay N 5595	MeSH
Moranoline	MeSH
1-Deoxymannojirimycin	MeSH

Chemical Formula

C₆H₁₃NO₄

Average Mass

163.1717 Da

Monoisotopic Mass

163.08446 Da

IUPAC Name

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

Traditional Name

deoxymannojirimycin

CAS Registry Number

Not Available

SMILES

OC[C@H]1NC[C@@H](O)[C@@H](O)[C@@H]1O

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-KVTDHHQDSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Adenophora triphylla	LOTUS Database	35616633
Adenophora triphylla var.japonica	KNApSAcK Database	22123792
Agrobacterium	NPAtlas	2547743
Albizia myriophylla	KNApSAcK Database	22123792
Angylocalyx pynaertii	LOTUS Database	35616633
Angylocalyx spp.	KNApSAcK Database	22123792
Bacillus amyloliquefaciens	Bacteria	KNApSAcK
Bacillus polymyxa	Bacteria	KNApSAcK
Bacillus subtilis	Bacteria	KNApSAcK
Commelina communis	LOTUS Database	35616633
Commelina communis L	Plant	KNApSAcK
Connarus ferrugineus	KNApSAcK Database	22123792
Derris malaccensis	KNApSAcK Database	22123792
Endospermum medullosum	KNApSAcK Database	22123792
Hyacinthus orientalis	KNApSAcK Database	22123792
Lonchocarpus costaricensis	KNApSAcK Database	22123792
Lonchocarpus sericeus	KNApSAcK Database	22123792
Morus bombycis	Plant	KNApSAcK
Morus spp.	Plant	KNApSAcK
Murus sp.	-	KNApSAcK
Omphalea diandra	KNApSAcK Database	22123792
Omphalea queenslandiae	Plant	KNApSAcK
Streptomyces lavandulae subsp. trehalostaticus no.2882	Bacteria	KNApSAcK

Species Where Detected

Species Name	Source	Reference
Agrobacterium sp. No.19-1	KNApSAcK Database	22123792
Streptomyces lavandulae GC-148	KNApSAcK Database	22123792

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as piperidines. These 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:41938 )
Piperidine alkaloids (C10141 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
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	15.84 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

External Links

NPAtlas ID

NPA020720

HMDB ID

Not Available

DrugBank ID

DB03955

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00002035

Chemspider ID

65214

KEGG Compound ID

C10141

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

72258

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Furumoto T, Asano N, Kameda Y, Matsui K: Microbial epimerization of 1-deoxynojirimycin to 1-deoxymannojirimycin. J Antibiot (Tokyo). 1989 Aug;42(8):1302-3. doi: 10.7164/antibiotics.42.1302. [PubMed:2547743 ]

Showing NP-Card for 1-deoxymannojirimycin (NP0013553)

MOL for NP0013553 (1-deoxymannojirimycin)

3D MOL for NP0013553 (1-deoxymannojirimycin)

3D SDF for NP0013553 (1-deoxymannojirimycin)

3D-SDF for NP0013553 (1-deoxymannojirimycin)

PDB for NP0013553 (1-deoxymannojirimycin)

3D PDB for NP0013553 (1-deoxymannojirimycin)

SMILES for NP0013553 (1-deoxymannojirimycin)

INCHI for NP0013553 (1-deoxymannojirimycin)

Structure for NP0013553 (1-deoxymannojirimycin)

3D Structure for NP0013553 (1-deoxymannojirimycin)