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Showing NP-Card for 3-epi-fagomine (NP0314904)

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Record Information
Version2.0
Created at2022-09-11 13:16:01 UTC
Updated at2022-09-11 13:16:01 UTC
NP-MRD IDNP0314904
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-epi-fagomine
Description3-Epi-fagomine 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. 3-epi-fagomine is found in Bombyx mori, Morus alba and Xanthocercis zambesiaca. 3-epi-fagomine was first documented in 1994 (PMID: 8050098). 3-Epi-fagomine is a very strong basic compound (based on its pKa) (PMID: 18323202) (PMID: 22207282) (PMID: 9157194) (PMID: 9544568).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0314904 (3-epi-fagomine)


  Mrv1652309272007292D          

 10 10  0  0  0  0            999 V2000
   -0.8035    1.5169    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5180    1.1044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5180    0.2793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8035   -0.1330    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0890    0.2793    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0890    1.1044    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6253   -0.1331    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6253    1.5169    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8035    2.3419    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6253   -0.9581    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  5  6  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  7  1  1  0  0  0
  1  9  1  6  0  0  0
  6  8  1  6  0  0  0
  7 10  1  0  0  0  0
M  END
Download

3D MOL for NP0314904 (3-epi-fagomine)

     RDKit          3D

 23 23  0  0  0  0  0  0  0  0999 V2000
    2.5717    0.2872    0.8083 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2070   -0.6047   -0.2144 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6953   -0.6856   -0.3599 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1679   -1.1444    0.8914 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2599   -1.2228    0.9419 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8667    0.0330    0.3731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8113    1.0941    0.3434 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2725    2.3651    0.1832 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1877    0.6727   -0.7318 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5579    0.5314   -1.9230 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2418    0.9534    0.4809 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6922   -0.3291   -1.1735 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6349   -1.5943    0.0885 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4997   -1.4363   -1.1463 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6704   -1.9180    1.3151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6694   -2.1415    0.4763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5504   -1.2524    2.0234 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1367   -0.2056   -0.6959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7711    0.3247    0.9496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2528    1.0308    1.3067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8846    2.5014   -0.5556 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9721    1.4156   -0.8953 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5076    1.3256   -2.4860 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
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  3  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  6
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
  6 19  1  0
  7 20  1  1
  8 21  1  0
  9 22  1  6
 10 23  1  0
M  END
Download

3D SDF for NP0314904 (3-epi-fagomine)


  Mrv1652309272007292D          

 10 10  0  0  0  0            999 V2000
   -0.8035    1.5169    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5180    1.1044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5180    0.2793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8035   -0.1330    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0890    0.2793    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0890    1.1044    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6253   -0.1331    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6253    1.5169    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8035    2.3419    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6253   -0.9581    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  5  6  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  7  1  1  0  0  0
  1  9  1  6  0  0  0
  6  8  1  6  0  0  0
  7 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0314904

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H13NO3/c8-3-4-6(10)5(9)1-2-7-4/h4-10H,1-3H2/t4-,5+,6-/m1/s1

> <INCHI_KEY>
YZNNBIPIQWYLDM-NGJCXOISSA-N

> <FORMULA>
C6H13NO3

> <MOLECULAR_WEIGHT>
147.174

> <EXACT_MASS>
147.089543283

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
14.863475971279112

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.55

> <JCHEM_LOGP>
-2.195448502

> <ALOGPS_LOGS>
0.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.792558102359045

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.431832079316841

> <JCHEM_PKA_STRONGEST_BASIC>
8.630686174074768

> <JCHEM_POLAR_SURFACE_AREA>
72.72

> <JCHEM_REFRACTIVITY>
35.4773

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.73e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S)-2-(hydroxymethyl)piperidine-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0314904 (3-epi-fagomine)

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PDB for NP0314904 (3-epi-fagomine)
HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  C   UNK     0      -1.500   2.832   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.834   2.062   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.834   0.521   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -1.500  -0.248   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -0.166   0.521   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.166   2.062   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.167  -0.248   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.167   2.832   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.500   4.372   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.167  -1.788   0.000  0.00  0.00           O+0
CONECT    1    2    6    9                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    6    4    7                                                  
CONECT    6    1    5    8                                                  
CONECT    7    5   10                                                       
CONECT    8    6                                                            
CONECT    9    1                                                            
CONECT   10    7                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

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3D PDB for NP0314904 (3-epi-fagomine)
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SMILES for NP0314904 (3-epi-fagomine)
OC[C@H]1NCC[C@H](O)[C@@H]1O
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INCHI for NP0314904 (3-epi-fagomine)
InChI=1S/C6H13NO3/c8-3-4-6(10)5(9)1-2-7-4/h4-10H,1-3H2/t4-,5+,6-/m1/s1
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View in JSmol
Synonyms
ValueSource
3-EpifagomineChEBI
D-3-epi-FagominePhytoBank
(2R,3R,4S)-2-(Hydroxymethyl)-3,4-piperidinediolPhytoBank
Chemical FormulaC6H13NO3
Average Mass147.1740 Da
Monoisotopic Mass147.08954 Da
IUPAC Name(2R,3R,4S)-2-(hydroxymethyl)piperidine-3,4-diol
Traditional Name(2R,3R,4S)-2-(hydroxymethyl)piperidine-3,4-diol
CAS Registry NumberNot Available
SMILES
OC[C@H]1NCC[C@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C6H13NO3/c8-3-4-6(10)5(9)1-2-7-4/h4-10H,1-3H2/t4-,5+,6-/m1/s1
InChI KeyYZNNBIPIQWYLDM-NGJCXOISSA-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
Bombyx moriLOTUS Database
Morus albaLOTUS Database
Xanthocercis zambesiacaLOTUS 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
    • 

  • 1,2-diol
    • 

  • Secondary alcohol
    • 

  • Secondary aliphatic amine
    • 

  • Azacycle
    • 

  • Secondary amine
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic nitrogen compound
    • 

  • Amine
    • 

  • Primary alcohol
    • 

  • Organic oxygen compound
    • 

  • Alcohol
    • 

  • 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-1.6ALOGPS
logP-2.2ChemAxon
logS0.59ALOGPS
pKa (Strongest Acidic)13.43ChemAxon
pKa (Strongest Basic)8.63ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area72.72 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity35.48 m³·mol⁻¹ChemAxon
Polarizability14.86 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00049947  
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10290867  
PDB IDNot Available
ChEBI ID132399  
Good Scents IDNot Available
References
General References
  1. Zhou GX, Ruan JW, Huang MY, Ye WC, He YW: [Alkaloid constituents from silkworm dropping of Bombyx mori]. Zhong Yao Cai. 2007 Nov;30(11):1384-5. [PubMed:18323202  ] 
  2. Amezqueta S, Galan E, Fuguet E, Carrascal M, Abian J, Torres JL: Determination of D-fagomine in buckwheat and mulberry by cation exchange HPLC/ESI-Q-MS. Anal Bioanal Chem. 2012 Feb;402(5):1953-60. doi: 10.1007/s00216-011-5639-2. Epub  2011 Dec 30. [PubMed:22207282  ] 
  3. Asano N, Oseki K, Tomioka E, Kizu H, Matsui K: N-containing sugars from Morus alba and their glycosidase inhibitory activities. Carbohydr Res. 1994 Jun 17;259(2):243-55. doi: 10.1016/0008-6215(94)84060-1. [PubMed:8050098  ] 
  4. Kato A, Asano N, Kizu H, Matsui K: Fagomine isomers and glycosides from Xanthocercis zambesiaca. J Nat Prod. 1997 Mar;60(3):312-4. doi: 10.1021/np960646y. [PubMed:9157194  ] 
  5. Nojima H, Kimura I, Chen FJ, Sugihara Y, Haruno M, Kato A, Asano N: Antihyperglycemic effects of N-containing sugars from Xanthocercis zambesiaca, Morus bombycis, Aglaonema treubii, and Castanospermum australe in streptozotocin-diabetic mice. J Nat Prod. 1998 Mar;61(3):397-400. doi: 10.1021/np970277l. [PubMed:9544568  ] 
  6. LOTUS database [Link]