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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 00:17:48 UTC

Update Date

2022-03-07 02:56:00 UTC

HMDB ID

HMDB0038949

Secondary Accession Numbers

HMDB38949

Metabolite Identification

Common Name

3beta,6beta-Dihydroxynortropane

Description

3beta,6beta-Dihydroxynortropane 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. 3beta,6beta-Dihydroxynortropane has been detected, but not quantified in, fruits. This could make 3beta,6beta-dihydroxynortropane a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 3beta,6beta-Dihydroxynortropane.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
3b,6b-Dihydroxynortropane	Generator
3Β,6β-dihydroxynortropane	Generator

Chemical Formula

C₇H₁₃NO₂

Average Molecular Weight

143.1836

Monoisotopic Molecular Weight

143.094628665

IUPAC Name

8-azabicyclo[3.2.1]octane-3,6-diol

Traditional Name

8-azabicyclo[3.2.1]octane-3,6-diol

CAS Registry Number

Not Available

SMILES

OC1CC2CC(O)CC1N2

InChI Identifier

InChI=1S/C7H13NO2/c9-5-1-4-2-7(10)6(3-5)8-4/h4-10H,1-3H2

InChI Key

MVUIPZFMWQBRCM-UHFFFAOYSA-N

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
Secondary alcohol
1,2-aminoalcohol
Azacycle
Organoheterocyclic compound
Secondary amine
Secondary aliphatic amine
Organic oxygen compound
Alcohol
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Amine
Hydrocarbon derivative
Organopnictogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0038949)
Cytoplasm (HMDB: HMDB0038949)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0038949)

Source

Exogenous

Exogenous (HMDB: HMDB0038949)

Food

Food (HMDB: HMDB0038949)

Fruit

Fruits (FooDB: FOOD00871)

Endogenous

Plant

Plant (HMDB: HMDB0038949)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0038949)

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	430 g/L	ALOGPS
logP	-0.71	ALOGPS
logP	-1.5	ChemAxon
logS	0.48	ALOGPS
pKa (Strongest Acidic)	14.45	ChemAxon
pKa (Strongest Basic)	10.02	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	52.49 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	36.62 m³·mol⁻¹	ChemAxon
Polarizability	14.96 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	130.737	31661259
DarkChem	[M-H]-	125.793	31661259
DeepCCS	[M+H]+	132.212	30932474
DeepCCS	[M-H]-	130.118	30932474
DeepCCS	[M-2H]-	166.187	30932474
DeepCCS	[M+Na]+	140.958	30932474
AllCCS	[M+H]+	134.4	32859911
AllCCS	[M+H-H2O]+	129.9	32859911
AllCCS	[M+NH4]+	138.6	32859911
AllCCS	[M+Na]+	139.8	32859911
AllCCS	[M-H]-	127.8	32859911
AllCCS	[M+Na-2H]-	129.0	32859911
AllCCS	[M+HCOO]-	130.5	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022.	1.02 minutes	32390414
Predicted by Siyang on May 30, 2022	8.1658 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	5.98 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	402.5 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	385.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	259.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	52.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	172.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	54.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	280.4 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	224.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	779.0 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	526.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	37.1 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	593.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	191.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	234.8 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	876.2 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	597.9 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	328.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3beta,6beta-Dihydroxynortropane	OC1CC2CC(O)CC1N2	2551.3	Standard polar	33892256
3beta,6beta-Dihydroxynortropane	OC1CC2CC(O)CC1N2	1390.6	Standard non polar	33892256
3beta,6beta-Dihydroxynortropane	OC1CC2CC(O)CC1N2	1553.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3beta,6beta-Dihydroxynortropane,1TMS,isomer #1	C[Si](C)(C)OC1CC2CC(O)CC1N2	1519.7	Semi standard non polar	33892256
3beta,6beta-Dihydroxynortropane,1TMS,isomer #2	C[Si](C)(C)OC1CC2CC(O)C(C1)N2	1450.6	Semi standard non polar	33892256
3beta,6beta-Dihydroxynortropane,1TMS,isomer #3	C[Si](C)(C)N1C2CC(O)CC1C(O)C2	1537.1	Semi standard non polar	33892256
3beta,6beta-Dihydroxynortropane,2TMS,isomer #1	C[Si](C)(C)OC1CC2CC(O[Si](C)(C)C)C(C1)N2	1531.6	Semi standard non polar	33892256
3beta,6beta-Dihydroxynortropane,2TMS,isomer #2	C[Si](C)(C)OC1CC2CC(O)CC1N2[Si](C)(C)C	1599.6	Semi standard non polar	33892256
3beta,6beta-Dihydroxynortropane,2TMS,isomer #3	C[Si](C)(C)OC1CC2CC(O)C(C1)N2[Si](C)(C)C	1563.7	Semi standard non polar	33892256
3beta,6beta-Dihydroxynortropane,3TMS,isomer #1	C[Si](C)(C)OC1CC2CC(O[Si](C)(C)C)C(C1)N2[Si](C)(C)C	1636.5	Semi standard non polar	33892256
3beta,6beta-Dihydroxynortropane,3TMS,isomer #1	C[Si](C)(C)OC1CC2CC(O[Si](C)(C)C)C(C1)N2[Si](C)(C)C	1684.5	Standard non polar	33892256
3beta,6beta-Dihydroxynortropane,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1CC2CC(O)CC1N2	1749.4	Semi standard non polar	33892256
3beta,6beta-Dihydroxynortropane,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC2CC(O)C(C1)N2	1728.2	Semi standard non polar	33892256
3beta,6beta-Dihydroxynortropane,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1C2CC(O)CC1C(O)C2	1780.4	Semi standard non polar	33892256
3beta,6beta-Dihydroxynortropane,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1CC2CC(O[Si](C)(C)C(C)(C)C)C(C1)N2	1996.0	Semi standard non polar	33892256
3beta,6beta-Dihydroxynortropane,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1CC2CC(O)CC1N2[Si](C)(C)C(C)(C)C	2067.4	Semi standard non polar	33892256
3beta,6beta-Dihydroxynortropane,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC1CC2CC(O)C(C1)N2[Si](C)(C)C(C)(C)C	2021.7	Semi standard non polar	33892256
3beta,6beta-Dihydroxynortropane,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1CC2CC(O[Si](C)(C)C(C)(C)C)C(C1)N2[Si](C)(C)C(C)(C)C	2300.3	Semi standard non polar	33892256
3beta,6beta-Dihydroxynortropane,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1CC2CC(O[Si](C)(C)C(C)(C)C)C(C1)N2[Si](C)(C)C(C)(C)C	2361.7	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3beta,6beta-Dihydroxynortropane GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9400000000-bcdd4fb5cbe650393d8d	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3beta,6beta-Dihydroxynortropane GC-MS (2 TMS) - 70eV, Positive	splash10-00di-5920000000-801ac2d07416bfbc0051	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3beta,6beta-Dihydroxynortropane GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta,6beta-Dihydroxynortropane 10V, Positive-QTOF	splash10-004i-0900000000-401caabdecb84cf5b8bb	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta,6beta-Dihydroxynortropane 20V, Positive-QTOF	splash10-056r-0900000000-d298c10f938824a275ad	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta,6beta-Dihydroxynortropane 40V, Positive-QTOF	splash10-0a4i-5900000000-252fc3e81e1b672c6f69	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta,6beta-Dihydroxynortropane 10V, Negative-QTOF	splash10-0006-0900000000-4ec9c340f77f7f239fb4	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta,6beta-Dihydroxynortropane 20V, Negative-QTOF	splash10-00dl-0900000000-ddb7b3e7ef12ef235bb6	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta,6beta-Dihydroxynortropane 40V, Negative-QTOF	splash10-01pn-9400000000-b831ee3b9ca2297cb876	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta,6beta-Dihydroxynortropane 10V, Negative-QTOF	splash10-0006-0900000000-bf6e206b443f53ef90b5	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta,6beta-Dihydroxynortropane 20V, Negative-QTOF	splash10-0006-0900000000-7c968fdd779617dd021c	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta,6beta-Dihydroxynortropane 40V, Negative-QTOF	splash10-0006-9600000000-75f8dfc7e89685c46673	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta,6beta-Dihydroxynortropane 10V, Positive-QTOF	splash10-002f-0900000000-b23a665ccdcf103ea379	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta,6beta-Dihydroxynortropane 20V, Positive-QTOF	splash10-0a4i-0900000000-1b75f2635d6550c2c896	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3beta,6beta-Dihydroxynortropane 40V, Positive-QTOF	splash10-001i-9200000000-874c2803685118b62b51	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB018428

KNApSAcK ID

Not Available

Chemspider ID

20057355

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

22297531

PDB ID

Not Available

ChEBI ID

165179

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for 3beta,6beta-Dihydroxynortropane (HMDB0038949)

MOL for HMDB0038949 (3beta,6beta-Dihydroxynortropane)

3D MOL for HMDB0038949 (3beta,6beta-Dihydroxynortropane)

3D SDF for HMDB0038949 (3beta,6beta-Dihydroxynortropane)

3D-SDF for HMDB0038949 (3beta,6beta-Dihydroxynortropane)

PDB for HMDB0038949 (3beta,6beta-Dihydroxynortropane)

3D PDB for HMDB0038949 (3beta,6beta-Dihydroxynortropane)

SMILES for HMDB0038949 (3beta,6beta-Dihydroxynortropane)

INCHI for HMDB0038949 (3beta,6beta-Dihydroxynortropane)

Structure for HMDB0038949 (3beta,6beta-Dihydroxynortropane)

3D Structure for HMDB0038949 (3beta,6beta-Dihydroxynortropane)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra