Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 01:34:12 UTC

Update Date

2023-02-21 17:27:25 UTC

HMDB ID

HMDB0040021

Secondary Accession Numbers

HMDB40021

Metabolite Identification

Common Name

2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine

Description

2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine 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-5-(3-hydroxypropanoyl)-1H-pyrrolizine.

Structure

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


  Mrv0541 05061311342D          

 13 14  0  0  0  0            999 V2000
   -0.4849    1.4924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542    1.4924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2721    3.5576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.1599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5271    4.3422    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5692    2.1599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8242    2.9445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846    1.9049    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9751    4.9553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6312    3.1160    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  3  1  0  0  0  0
  6  1  1  0  0  0  0
  7  5  1  0  0  0  0
  8  2  1  0  0  0  0
  8  3  2  0  0  0  0
  9  4  2  0  0  0  0
 10  5  1  0  0  0  0
 10  9  1  0  0  0  0
 11  6  1  0  0  0  0
 11  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12  7  1  0  0  0  0
 13 10  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0040021

> <DATABASE_NAME>
hmdb

> <SMILES>
OCCC(=O)C1=CC=C2CCCN12

> <INCHI_IDENTIFIER>
InChI=1S/C10H13NO2/c12-7-5-10(13)9-4-3-8-2-1-6-11(8)9/h3-4,12H,1-2,5-7H2

> <INCHI_KEY>
DLLQYHQNPSDCSK-UHFFFAOYSA-N

> <FORMULA>
C10H13NO2

> <MOLECULAR_WEIGHT>
179.2157

> <EXACT_MASS>
179.094628665

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
19.537578375187707

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-(2,3-dihydro-1H-pyrrolizin-5-yl)-3-hydroxypropan-1-one

> <ALOGPS_LOGP>
0.84

> <JCHEM_LOGP>
0.4227701619999998

> <ALOGPS_LOGS>
-2.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.822049889110549

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.432975704423239

> <JCHEM_PKA_STRONGEST_BASIC>
-2.447487155422115

> <JCHEM_POLAR_SURFACE_AREA>
42.230000000000004

> <JCHEM_REFRACTIVITY>
50.33749999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.74e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-(6,7-dihydro-5H-pyrrolizin-3-yl)-3-hydroxypropan-1-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      -0.905   2.786   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.929   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.835   2.786   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.375   6.641   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   4.032   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.851   8.105   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.465   2.016   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.929   4.032   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.405   5.496   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       1.465   3.556   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0       1.820   9.250   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       4.912   5.817   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    8                                                       
CONECT    3    4    8                                                       
CONECT    4    3    9                                                       
CONECT    5    7   10                                                       
CONECT    6    1   11                                                       
CONECT    7    5   12                                                       
CONECT    8    2    3   11                                                  
CONECT    9    4   10   11                                                  
CONECT   10    5    9   13                                                  
CONECT   11    6    8    9                                                  
CONECT   12    7                                                            
CONECT   13   10                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END

COMPND    HMDB0040021
HETATM    1  O1  UNL     1       2.637   1.222   0.273  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.638   0.478   0.088  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.880  -0.911  -0.378  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.366  -1.168  -0.526  1.00  0.00           C  
HETATM    5  O2  UNL     1       4.042  -1.000   0.675  1.00  0.00           O  
HETATM    6  C4  UNL     1       0.286   0.972   0.325  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.018   2.250   0.754  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.388   2.316   0.857  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.927   1.100   0.498  1.00  0.00           C  
HETATM   10  N1  UNL     1      -0.895   0.304   0.181  1.00  0.00           N  
HETATM   11  C8  UNL     1      -1.415  -0.996  -0.200  1.00  0.00           C  
HETATM   12  C9  UNL     1      -2.771  -0.632  -0.767  1.00  0.00           C  
HETATM   13  C10 UNL     1      -3.220   0.343   0.329  1.00  0.00           C  
HETATM   14  H1  UNL     1       1.371  -1.666   0.239  1.00  0.00           H  
HETATM   15  H2  UNL     1       1.468  -0.971  -1.425  1.00  0.00           H  
HETATM   16  H3  UNL     1       3.474  -2.185  -0.942  1.00  0.00           H  
HETATM   17  H4  UNL     1       3.744  -0.432  -1.276  1.00  0.00           H  
HETATM   18  H5  UNL     1       4.937  -1.414   0.600  1.00  0.00           H  
HETATM   19  H6  UNL     1       0.708   3.036   0.963  1.00  0.00           H  
HETATM   20  H7  UNL     1      -1.991   3.155   1.162  1.00  0.00           H  
HETATM   21  H8  UNL     1      -0.791  -1.546  -0.904  1.00  0.00           H  
HETATM   22  H9  UNL     1      -1.612  -1.538   0.747  1.00  0.00           H  
HETATM   23  H10 UNL     1      -3.449  -1.477  -0.871  1.00  0.00           H  
HETATM   24  H11 UNL     1      -2.631  -0.028  -1.677  1.00  0.00           H  
HETATM   25  H12 UNL     1      -4.034   0.984   0.001  1.00  0.00           H  
HETATM   26  H13 UNL     1      -3.409  -0.196   1.274  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    6
CONECT    3    4   14   15
CONECT    4    5   16   17
CONECT    5   18
CONECT    6    7    7   10
CONECT    7    8   19
CONECT    8    9    9   20
CONECT    9   10   13
CONECT   10   11
CONECT   11   12   21   22
CONECT   12   13   23   24
CONECT   13   25   26
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
1-(2,3-dihydro-1H-Pyrrolizin-5-yl)-3-hydroxy-1-propanone	HMDB

Chemical Formula

C₁₀H₁₃NO₂

Average Molecular Weight

179.2157

Monoisotopic Molecular Weight

179.094628665

IUPAC Name

1-(2,3-dihydro-1H-pyrrolizin-5-yl)-3-hydroxypropan-1-one

Traditional Name

1-(6,7-dihydro-5H-pyrrolizin-3-yl)-3-hydroxypropan-1-one

CAS Registry Number

97073-09-1

SMILES

OCCC(=O)C1=CC=C2CCCN12

InChI Identifier

InChI=1S/C10H13NO2/c12-7-5-10(13)9-4-3-8-2-1-6-11(8)9/h3-4,12H,1-2,5-7H2

InChI Key

DLLQYHQNPSDCSK-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 ketone
Aryl alkyl ketone
Beta-hydroxy ketone
Substituted pyrrole
Pyrrole
Heteroaromatic compound
Ketone
Azacycle
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0040021)
Cytoplasm (HMDB: HMDB0040021)

Source

Exogenous

Food

Food (HMDB: HMDB0040021)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0040021)

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	6923 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	1.74 g/L	ALOGPS
logP	0.84	ALOGPS
logP	0.42	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	15.43	ChemAxon
pKa (Strongest Basic)	-2.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	42.23 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	50.34 m³·mol⁻¹	ChemAxon
Polarizability	19.54 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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]+	140.056	31661259
DarkChem	[M-H]-	137.41	31661259
DeepCCS	[M-2H]-	171.197	30932474
DeepCCS	[M+Na]+	146.735	30932474
AllCCS	[M+H]+	139.4	32859911
AllCCS	[M+H-H2O]+	135.0	32859911
AllCCS	[M+NH4]+	143.5	32859911
AllCCS	[M+Na]+	144.7	32859911
AllCCS	[M-H]-	142.5	32859911
AllCCS	[M+Na-2H]-	143.0	32859911
AllCCS	[M+HCOO]-	143.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine	OCCC(=O)C1=CC=C2CCCN12	2356.5	Standard polar	33892256
2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine	OCCC(=O)C1=CC=C2CCCN12	1711.8	Standard non polar	33892256
2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine	OCCC(=O)C1=CC=C2CCCN12	1754.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine,1TMS,isomer #1	C[Si](C)(C)OCCC(=O)C1=CC=C2CCCN21	1812.9	Semi standard non polar	33892256
2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCCC(=O)C1=CC=C2CCCN21	2056.8	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-5-(3-hydroxypropanoyl)-1H-pyrrolizine GC-MS (Non-derivatized) - 70eV, Positive	splash10-053u-9700000000-f5a2a208332e91c1a1a2	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine GC-MS (1 TMS) - 70eV, Positive	splash10-0089-8910000000-266f21a7375dbfd2d5d2	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine 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-5-(3-hydroxypropanoyl)-1H-pyrrolizine 10V, Positive-QTOF	splash10-03e9-0900000000-fde8e8da2ca19ed91304	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine 20V, Positive-QTOF	splash10-08fr-0900000000-f9c54919e910532ca867	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine 40V, Positive-QTOF	splash10-0a4i-3900000000-4015309cec230711c176	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine 10V, Negative-QTOF	splash10-004i-0900000000-cd2ac70bb31d73f63eda	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine 20V, Negative-QTOF	splash10-0032-0900000000-750ef9a4759db0b7f2bc	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine 40V, Negative-QTOF	splash10-001j-6900000000-eab07f10b4f3e2bcb457	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine 10V, Negative-QTOF	splash10-004i-0900000000-9723bb588a00234faf36	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine 20V, Negative-QTOF	splash10-0a4i-2900000000-64b57a8bfb49d4174e53	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine 40V, Negative-QTOF	splash10-066u-9400000000-eade6e4501ab9d07a27d	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine 10V, Positive-QTOF	splash10-001i-0900000000-7b53bdd2d1431e106292	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine 20V, Positive-QTOF	splash10-053r-0900000000-80030337003ef514d9dd	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine 40V, Positive-QTOF	splash10-052f-9500000000-b97a631ce90e8c4e23ff	2021-09-25	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+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

FDB019703

KNApSAcK ID

Not Available

Chemspider ID

4934353

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6428976

PDB ID

Not Available

ChEBI ID

173504

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1881541

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-5-(3-hydroxypropanoyl)-1H-pyrrolizine (HMDB0040021)

MOL for HMDB0040021 (2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine)

3D MOL for HMDB0040021 (2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine)

3D SDF for HMDB0040021 (2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine)

3D-SDF for HMDB0040021 (2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine)

PDB for HMDB0040021 (2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine)

3D PDB for HMDB0040021 (2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine)

SMILES for HMDB0040021 (2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine)

INCHI for HMDB0040021 (2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine)

Structure for HMDB0040021 (2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine)

3D Structure for HMDB0040021 (2,3-Dihydro-5-(3-hydroxypropanoyl)-1H-pyrrolizine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra