NP-MRD: Showing NP-Card for (1s,2r,3s,4r,5s)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol (NP0159141)

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Record Information

Version

2.0

Created at

2022-09-02 16:51:00 UTC

Updated at

2022-09-02 16:51:01 UTC

NP-MRD ID

NP0159141

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,2r,3s,4r,5s)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol

Description

Calystegine B2, also known as calystegine b(3), belongs to the class of organic compounds known as tropane alkaloids. These are organic compounds containing the nitrogenous bicyclic alkaloid parent N-Methyl-8-azabicyclo[3.2.1]Octane. (1s,2r,3s,4r,5s)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol is found in Acherontia atropos. (1s,2r,3s,4r,5s)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol was first documented in 2012 (PMID: 22148579). Based on a literature review a significant number of articles have been published on Calystegine B2 (PMID: 35845638) (PMID: 30579118) (PMID: 30245074) (PMID: 27161660) (PMID: 24657053) (PMID: 23697377).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309022218512D          

 12 13  0  0  1  0            999 V2000
    3.6130    0.6363    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7880    0.6363    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4300    1.3796    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9444    2.0247    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6257    1.5632    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9807    1.0488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9807    0.2238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6257   -0.2905    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4421   -1.0949    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3940    0.6363    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4300   -0.1070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9444   -0.7520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
  5 10  1  6  0  0  0
  8 11  1  0  0  0  0
  2 11  1  0  0  0  0
 11 12  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0159141

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1[C@@H]2CC[C@@](O)(N2)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C7H13NO4/c9-4-3-1-2-7(12,8-3)6(11)5(4)10/h3-6,8-12H,1-2H2/t3-,4+,5-,6+,7-/m0/s1

> <INCHI_KEY>
FXFBVZOJVHCEDO-FHKSGDNWSA-N

> <FORMULA>
C7H13NO4

> <MOLECULAR_WEIGHT>
175.184

> <EXACT_MASS>
175.084457903

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
16.64159480225517

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,3S,4R,5S)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol

> <ALOGPS_LOGP>
-1.81

> <JCHEM_LOGP>
-2.148462142

> <ALOGPS_LOGS>
0.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.075446024332724

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.129613675619893

> <JCHEM_PKA_STRONGEST_BASIC>
8.572879603048014

> <JCHEM_POLAR_SURFACE_AREA>
92.95

> <JCHEM_REFRACTIVITY>
39.071

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.33e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,3S,4R,5S)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  O   UNK     0       6.744   1.188   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       5.204   1.188   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.536   2.575   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       5.496   3.779   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       3.035   2.918   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.831   1.958   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.831   0.418   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.035  -0.542   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.692  -2.044   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0       2.602   1.188   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       4.536  -0.200   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.496  -1.404   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10   11                                             
CONECT    9    8                                                            
CONECT   10    8    5                                                       
CONECT   11    8    2   12                                                  
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END

View in JSmol

Synonyms

Value	Source
1,2,3,4-Tetrahydroxy-nor-tropane	MeSH
Calystegine b(2)	MeSH
Calystegine b(3)	MeSH
Calystegine b(4)	MeSH
Calystegine b3	MeSH
Calystegine b4	MeSH

Chemical Formula

C₇H₁₃NO₄

Average Mass

175.1840 Da

Monoisotopic Mass

175.08446 Da

IUPAC Name

(1S,2R,3S,4R,5S)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol

Traditional Name

(1S,2R,3S,4R,5S)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol

CAS Registry Number

Not Available

SMILES

O[C@@H]1[C@@H]2CC[C@@](O)(N2)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C7H13NO4/c9-4-3-1-2-7(12,8-3)6(11)5(4)10/h3-6,8-12H,1-2H2/t3-,4+,5-,6+,7-/m0/s1

InChI Key

FXFBVZOJVHCEDO-FHKSGDNWSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Acherontia atropos	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tropane alkaloids. These are organic compounds containing the nitrogenous bicyclic alkaloid parent N-Methyl-8-azabicyclo[3.2.1]Octane.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Tropane alkaloids

Sub Class

Not Available

Direct Parent

Tropane alkaloids

Alternative Parents

Substituents

Tropane alkaloid
Piperidine
Cyclic alcohol
Pyrrolidine
Hemiaminal
Secondary alcohol
Alkanolamine
Secondary aliphatic amine
Polyol
Azacycle
Secondary amine
Organoheterocyclic compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organopnictogen compound
Alcohol
Hydrocarbon derivative
Amine
Organic nitrogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

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	-1.8	ALOGPS
logP	-2.1	ChemAxon
logS	0.62	ALOGPS
pKa (Strongest Acidic)	12.13	ChemAxon
pKa (Strongest Basic)	8.57	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	0	ChemAxon
Refractivity	39.07 m³·mol⁻¹	ChemAxon
Polarizability	16.64 Å³	ChemAxon
Number of Rings	2	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

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00002283

Chemspider ID

340555

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

384346

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Hampejsova R, Berka M, Berkova V, Jersakova J, Domkarova J, von Rundstedt F, Frary A, Saiz-Fernandez I, Brzobohaty B, Cerny M: Interaction With Fungi Promotes the Accumulation of Specific Defense Molecules in Orchid Tubers and May Increase the Value of Tubers for Biotechnological and Medicinal Applications: The Case Study of Interaction Between Dactylorhiza sp. and Tulasnella calospora. Front Plant Sci. 2022 Jun 30;13:757852. doi: 10.3389/fpls.2022.757852. eCollection 2022. [PubMed:35845638 ]
Underlin EN, Jensen HH: Synthesis of nortropane alkaloid calystegine B(2) from methyl alpha-d-xylopyranoside. Carbohydr Res. 2019 Jan 15;472:122-126. doi: 10.1016/j.carres.2018.12.002. Epub 2018 Dec 7. [PubMed:30579118 ]
Romera-Torres A, Romero-Gonzalez R, Martinez Vidal JL, Garrido Frenich A: Analysis of calystegines in tomato-based products by liquid chromatography-Orbitrap mass spectrometry. J Chromatogr A. 2018 Nov 16;1576:51-57. doi: 10.1016/j.chroma.2018.09.030. Epub 2018 Sep 17. [PubMed:30245074 ]
Wang HY, Kato A, Kinami K, Li YX, Fleet GW, Yu CY: Concise synthesis of calystegines B2 and B3via intramolecular Nozaki-Hiyama-Kishi reaction. Org Biomol Chem. 2016 Jun 7;14(21):4885-96. doi: 10.1039/c6ob00697c. Epub 2016 May 10. [PubMed:27161660 ]
Kato A, Nakagome I, Nakagawa S, Koike Y, Nash RJ, Adachi I, Hirono S: Docking and SAR studies of calystegines: binding orientation and influence on pharmacological chaperone effects for Gaucher's disease. Bioorg Med Chem. 2014 Apr 15;22(8):2435-41. doi: 10.1016/j.bmc.2014.02.057. Epub 2014 Mar 12. [PubMed:24657053 ]
Jockovic N, Fischer W, Brandsch M, Brandt W, Drager B: Inhibition of human intestinal alpha-glucosidases by calystegines. J Agric Food Chem. 2013 Jun 12;61(23):5550-7. doi: 10.1021/jf4010737. Epub 2013 Jun 3. [PubMed:23697377 ]
Kyne SH, Miles JA, Percy JM, Singh K: Executing and rationalizing the synthesis of a difluorinated analogue of a ring-expanded calystegine B2. J Org Chem. 2012 Jan 20;77(2):991-8. doi: 10.1021/jo2022845. Epub 2011 Dec 30. [PubMed:22148579 ]
LOTUS database [Link]

Showing NP-Card for (1s,2r,3s,4r,5s)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol (NP0159141)

MOL for NP0159141 ((1s,2r,3s,4r,5s)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol)

3D MOL for NP0159141 ((1s,2r,3s,4r,5s)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol)

3D SDF for NP0159141 ((1s,2r,3s,4r,5s)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol)

3D-SDF for NP0159141 ((1s,2r,3s,4r,5s)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol)

PDB for NP0159141 ((1s,2r,3s,4r,5s)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol)

3D PDB for NP0159141 ((1s,2r,3s,4r,5s)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol)

SMILES for NP0159141 ((1s,2r,3s,4r,5s)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol)

INCHI for NP0159141 ((1s,2r,3s,4r,5s)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol)

Structure for NP0159141 ((1s,2r,3s,4r,5s)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol)

3D Structure for NP0159141 ((1s,2r,3s,4r,5s)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol)