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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 22:05:20 UTC

Update Date

2021-09-26 22:53:06 UTC

HMDB ID

HMDB0244971

Secondary Accession Numbers

None

Metabolite Identification

Common Name

2-Amino-1,3-propanediol

Description

2-Amino-1,3-propanediol, also known as serinol or 2-aminopropane-1,3-diol, belongs to the class of organic compounds known as 1,2-aminoalcohols. These are organic compounds containing an alkyl chain with an amine group bound to the C1 atom and an alcohol group bound to the C2 atom. Based on a literature review a significant number of articles have been published on 2-Amino-1,3-propanediol. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-amino-1,3-propanediol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-Amino-1,3-propanediol is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Serinol, (+-)-isomer	HMDB
Serinol	HMDB
2-Aminopropane-1,3-diol	HMDB

Chemical Formula

C₃H₉NO₂

Average Molecular Weight

91.1091

Monoisotopic Molecular Weight

91.063328537

IUPAC Name

2-aminopropane-1,3-diol

Traditional Name

2-aminopropane-1,3-diol

CAS Registry Number

Not Available

SMILES

NC(CO)CO

InChI Identifier

InChI=1S/C3H9NO2/c4-3(1-5)2-6/h3,5-6H,1-2,4H2

InChI Key

KJJPLEZQSCZCKE-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,2-aminoalcohols. These are organic compounds containing an alkyl chain with an amine group bound to the C1 atom and an alcohol group bound to the C2 atom.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Amines

Direct Parent

1,2-aminoalcohols

Alternative Parents

Substituents

1,2-aminoalcohol
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Primary alcohol
Organooxygen compound
Primary aliphatic amine
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

a small molecule (CPD-9382 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

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
logP	-1.8	ALOGPS
logP	-1.9	ChemAxon
logS	1.06	ALOGPS
pKa (Strongest Acidic)	14.75	ChemAxon
pKa (Strongest Basic)	9.23	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	66.48 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	22.17 m³·mol⁻¹	ChemAxon
Polarizability	9.38 Å³	ChemAxon
Number of Rings	0	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
DeepCCS	[M+H]+	125.378	30932474
DeepCCS	[M-H]-	123.454	30932474
DeepCCS	[M-2H]-	159.054	30932474
DeepCCS	[M+Na]+	133.625	30932474
AllCCS	[M+H]+	125.3	32859911
AllCCS	[M+H-H2O]+	120.9	32859911
AllCCS	[M+NH4]+	129.3	32859911
AllCCS	[M+Na]+	130.5	32859911
AllCCS	[M-H]-	123.8	32859911
AllCCS	[M+Na-2H]-	128.4	32859911
AllCCS	[M+HCOO]-	133.5	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	8.6593 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	5.78 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	433.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	331.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	45.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	223.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	114.2 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	271.1 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	219.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	883.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	558.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	37.9 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	615.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	208.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	315.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	769.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	543.2 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	341.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Amino-1,3-propanediol	NC(CO)CO	1943.5	Standard polar	33892256
2-Amino-1,3-propanediol	NC(CO)CO	1047.7	Standard non polar	33892256
2-Amino-1,3-propanediol	NC(CO)CO	1140.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2-Amino-1,3-propanediol,3TMS,isomer #1	C[Si](C)(C)NC(CO[Si](C)(C)C)CO[Si](C)(C)C	1306.4	Semi standard non polar	33892256
2-Amino-1,3-propanediol,3TMS,isomer #1	C[Si](C)(C)NC(CO[Si](C)(C)C)CO[Si](C)(C)C	1369.1	Standard non polar	33892256
2-Amino-1,3-propanediol,3TMS,isomer #1	C[Si](C)(C)NC(CO[Si](C)(C)C)CO[Si](C)(C)C	1303.7	Standard polar	33892256
2-Amino-1,3-propanediol,3TMS,isomer #2	C[Si](C)(C)OCC(CO)N([Si](C)(C)C)[Si](C)(C)C	1454.5	Semi standard non polar	33892256
2-Amino-1,3-propanediol,3TMS,isomer #2	C[Si](C)(C)OCC(CO)N([Si](C)(C)C)[Si](C)(C)C	1411.8	Standard non polar	33892256
2-Amino-1,3-propanediol,3TMS,isomer #2	C[Si](C)(C)OCC(CO)N([Si](C)(C)C)[Si](C)(C)C	1453.1	Standard polar	33892256
2-Amino-1,3-propanediol,4TMS,isomer #1	C[Si](C)(C)OCC(CO[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	1527.5	Semi standard non polar	33892256
2-Amino-1,3-propanediol,4TMS,isomer #1	C[Si](C)(C)OCC(CO[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	1498.9	Standard non polar	33892256
2-Amino-1,3-propanediol,4TMS,isomer #1	C[Si](C)(C)OCC(CO[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	1340.7	Standard polar	33892256
2-Amino-1,3-propanediol,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC(CO[Si](C)(C)C(C)(C)C)CO[Si](C)(C)C(C)(C)C	1920.8	Semi standard non polar	33892256
2-Amino-1,3-propanediol,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC(CO[Si](C)(C)C(C)(C)C)CO[Si](C)(C)C(C)(C)C	1961.4	Standard non polar	33892256
2-Amino-1,3-propanediol,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC(CO[Si](C)(C)C(C)(C)C)CO[Si](C)(C)C(C)(C)C	1754.6	Standard polar	33892256
2-Amino-1,3-propanediol,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC(CO)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2063.0	Semi standard non polar	33892256
2-Amino-1,3-propanediol,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC(CO)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2047.1	Standard non polar	33892256
2-Amino-1,3-propanediol,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC(CO)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	1814.1	Standard polar	33892256
2-Amino-1,3-propanediol,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(CO[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2325.3	Semi standard non polar	33892256
2-Amino-1,3-propanediol,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(CO[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2288.3	Standard non polar	33892256
2-Amino-1,3-propanediol,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(CO[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	1863.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-1,3-propanediol GC-MS (Non-derivatized) - 70eV, Positive	splash10-01q9-9000000000-a1b8227c1e70a17dba3b	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-1,3-propanediol GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-1,3-propanediol GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-1,3-propanediol GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-1,3-propanediol GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-1,3-propanediol GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-1,3-propanediol GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-1,3-propanediol GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-1,3-propanediol GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-1,3-propanediol GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-1,3-propanediol GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Amino-1,3-propanediol GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-03	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 - 2-Amino-1,3-propanediol 10V, Positive-QTOF	splash10-006x-9000000000-d794dbfc01f2a191c843	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-1,3-propanediol 20V, Positive-QTOF	splash10-05fu-9000000000-3932a831e52f4aaa2a1b	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-1,3-propanediol 40V, Positive-QTOF	splash10-0a4i-9000000000-cba8d8c310a3480e1d64	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-1,3-propanediol 10V, Negative-QTOF	splash10-0006-9000000000-10dbbdfb5601ef02ef86	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-1,3-propanediol 20V, Negative-QTOF	splash10-006x-9000000000-1badca82931fb49caa04	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-1,3-propanediol 40V, Negative-QTOF	splash10-052f-9000000000-ad9f27f4f98aa38719bd	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-1,3-propanediol 10V, Positive-QTOF	splash10-00dl-9000000000-cd2a8fa7da1095a74ee4	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-1,3-propanediol 20V, Positive-QTOF	splash10-05fu-9000000000-0c027a903789b1a1d402	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-1,3-propanediol 40V, Positive-QTOF	splash10-052f-9000000000-1f386df8670b3c04a1d7	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-1,3-propanediol 10V, Negative-QTOF	splash10-0a4i-9000000000-6e52909293d21f3f210b	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-1,3-propanediol 20V, Negative-QTOF	splash10-0a4i-9000000000-46131b507aa8bb44d9f8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2-Amino-1,3-propanediol 40V, Negative-QTOF	splash10-052f-9000000000-2359f5fc8b1198d004c9	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

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

Not Available

KNApSAcK ID

C00053952

Chemspider ID

61591

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

68294

PDB ID

Not Available

ChEBI ID

Not Available

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for 2-Amino-1,3-propanediol (HMDB0244971)

MOL for HMDB0244971 (2-Amino-1,3-propanediol)

3D MOL for HMDB0244971 (2-Amino-1,3-propanediol)

3D SDF for HMDB0244971 (2-Amino-1,3-propanediol)

3D-SDF for HMDB0244971 (2-Amino-1,3-propanediol)

PDB for HMDB0244971 (2-Amino-1,3-propanediol)

3D PDB for HMDB0244971 (2-Amino-1,3-propanediol)

SMILES for HMDB0244971 (2-Amino-1,3-propanediol)

INCHI for HMDB0244971 (2-Amino-1,3-propanediol)

Structure for HMDB0244971 (2-Amino-1,3-propanediol)

3D Structure for HMDB0244971 (2-Amino-1,3-propanediol)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra