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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 01:33:32 UTC

Update Date

2023-02-21 17:27:23 UTC

HMDB ID

HMDB0040008

Secondary Accession Numbers

HMDB40008

Metabolite Identification

Common Name

2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde

Description

2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde belongs to the class of organic compounds known as pyrrolizines. Pyrrolizines are compounds containing a pyrrolizine moiety, which consists of a pyrrole ring fused to a pyrrolidine ring. Based on a literature review very few articles have been published on 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
5-Formyl-2,3-dihydro-1H-pyrrolizine	HMDB

Chemical Formula

C₈H₉NO

Average Molecular Weight

135.1632

Monoisotopic Molecular Weight

135.068413915

IUPAC Name

2,3-dihydro-1H-pyrrolizine-5-carbaldehyde

Traditional Name

6,7-dihydro-5H-pyrrolizine-3-carbaldehyde

CAS Registry Number

6225-59-8

SMILES

O=CC1=CC=C2CCCN12

InChI Identifier

InChI=1S/C8H9NO/c10-6-8-4-3-7-2-1-5-9(7)8/h3-4,6H,1-2,5H2

InChI Key

XDRGCZAFSAFSLR-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrrolizines. Pyrrolizines are compounds containing a pyrrolizine moiety, which consists of a pyrrole ring fused to a pyrrolidine ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrrolizines

Sub Class

Not Available

Direct Parent

Pyrrolizines

Alternative Parents

Substituents

Pyrrolizine
Aryl-aldehyde
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aldehyde
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0040008)
Cytoplasm (HMDB: HMDB0040008)

Source

Exogenous

Exogenous (HMDB: HMDB0040008)

Food

Food (HMDB: HMDB0040008)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0040008)

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	1.54 g/L	ALOGPS
logP	1.22	ALOGPS
logP	1.16	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Basic)	-7.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	22 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	40.12 m³·mol⁻¹	ChemAxon
Polarizability	14.57 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	126.324	31661259
DarkChem	[M-H]-	124.992	31661259
DeepCCS	[M-2H]-	163.397	30932474
DeepCCS	[M+Na]+	138.399	30932474
AllCCS	[M+H]+	127.1	32859911
AllCCS	[M+H-H2O]+	122.3	32859911
AllCCS	[M+NH4]+	131.6	32859911
AllCCS	[M+Na]+	132.9	32859911
AllCCS	[M-H]-	127.6	32859911
AllCCS	[M+Na-2H]-	128.7	32859911
AllCCS	[M+HCOO]-	130.0	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.	3.03 minutes	32390414
Predicted by Siyang on May 30, 2022	12.3796 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.86 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	30.0 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1552.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	446.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	146.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	264.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	116.7 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	441.5 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	484.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	125.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	992.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	315.5 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	1148.4 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	277.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	378.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	466.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	416.2 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	90.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde	O=CC1=CC=C2CCCN12	1919.8	Standard polar	33892256
2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde	O=CC1=CC=C2CCCN12	1307.9	Standard non polar	33892256
2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde	O=CC1=CC=C2CCCN12	1361.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4r-5900000000-930f8c76a329dc84f6d3	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde 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 - 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde 10V, Positive-QTOF	splash10-000i-0900000000-c033d98cbdf5b5d6cbf6	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde 20V, Positive-QTOF	splash10-052r-0900000000-2aaa50019f79d029aa53	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde 40V, Positive-QTOF	splash10-0a4l-9600000000-c16d130d3439fdf1b5d6	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde 10V, Negative-QTOF	splash10-001i-0900000000-f56019a2fcc453dbecb7	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde 20V, Negative-QTOF	splash10-001i-0900000000-f5f5c17b96d0a4bdd044	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde 40V, Negative-QTOF	splash10-0ldi-8900000000-4a5256b235d4eb8c9d21	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde 10V, Negative-QTOF	splash10-053r-0900000000-f35812d6ac4f29adcb04	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde 20V, Negative-QTOF	splash10-0a4i-1900000000-94ef293714234b0a44f0	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde 40V, Negative-QTOF	splash10-017i-9200000000-b498f62f8a5ed30e556b	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde 10V, Positive-QTOF	splash10-000i-0900000000-adb607939c98cdbcaa70	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde 20V, Positive-QTOF	splash10-052r-1900000000-dbcc926dc75849cb2c11	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde 40V, Positive-QTOF	splash10-004l-9100000000-3eaff1951a2fabee0ec3	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

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

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX 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

FDB019690

KNApSAcK ID

Not Available

Chemspider ID

4933547

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6428138

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

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

Showing metabocard for 2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde (HMDB0040008)

MOL for HMDB0040008 (2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde)

3D MOL for HMDB0040008 (2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde)

3D SDF for HMDB0040008 (2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde)

3D-SDF for HMDB0040008 (2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde)

PDB for HMDB0040008 (2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde)

3D PDB for HMDB0040008 (2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde)

SMILES for HMDB0040008 (2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde)

INCHI for HMDB0040008 (2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde)

Structure for HMDB0040008 (2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde)

3D Structure for HMDB0040008 (2,3-Dihydro-1H-pyrrolizine-5-carboxaldehyde)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra