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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (4) Show 4 proteins XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2021-09-14 15:38:57 UTC

HMDB ID

HMDB0001369

Secondary Accession Numbers

HMDB01369

Metabolite Identification

Common Name

Pyrroline hydroxycarboxylic acid

Description

Pyrroline hydroxycarboxylic acid is a metabolite identified in the urine of patients with type II hyperprolinemia. (OMIM 239510 ). The urinary excretion of Pyrroline hydroxycarboxylic acid increased in hyperprolinemic patients but not in healthy controls during oral loading of hydroxyproline and hydroxyproline-ornithine. (PMID: 533224 ). Hyperprolinemia type II (HP II) is a rare inherited metabolic disease due to the deficiency of pyroline-5-carboxylate dehydrogenase. It is generally believed to be a benign condition although some patients have neurological problems such as refractory convulsions. (PMID: 15214748 ). The oxidation of pyrroline-carboxylate generates glutamate and pyrroline-hydroxycarboxylate, a reaction catalyzed by hydroxyproline oxidase (PMID: 500817 ).

Structure

MOL SDF 3D SDF PDB 3D PDB SMILES InChI

COMPND    https://cactus.nci.nih.gov/chemical/structure/OC1CC(N=C1)C(O)=O/file?format=s... 
AUTHOR    GENERATED BY OPEN BABEL 3.1.0
ATOM      1  OD  HYP A   1       2.784   0.777  -0.327  1.00  0.00           O  
ATOM      2  CG  HYP A   1       1.853   0.145   0.553  1.00  0.00           C  
ATOM      3  CB  HYP A   1       0.515   0.922   0.579  1.00  0.00           C  
ATOM      4  CA  HYP A   1      -0.298   0.135  -0.477  1.00  0.00           C  
ATOM      5  N   HYP A   1       0.316  -1.197  -0.515  1.00  0.00           N  
ATOM      6  CD  HYP A   1       1.468  -1.220   0.028  1.00  0.00           C  
ATOM      7  C   HYP A   1      -1.742   0.034  -0.057  1.00  0.00           C  
ATOM      8  O   HYP A   1      -2.572   1.070  -0.255  1.00  0.00           O  
ATOM      9  OXT HYP A   1      -2.152  -0.980   0.457  1.00  0.00           O  
ATOM     10  HD  HYP A   1       3.640   0.331  -0.381  1.00  0.00           H  
ATOM     11  HG  HYP A   1       2.270   0.067   1.557  1.00  0.00           H  
ATOM     12  HB1 HYP A   1       0.044   0.864   1.560  1.00  0.00           H  
ATOM     13  HB2 HYP A   1       0.656   1.959   0.274  1.00  0.00           H  
ATOM     14  HA  HYP A   1      -0.219   0.617  -1.451  1.00  0.00           H  
ATOM     15  HD  HYP A   1       2.089  -2.100   0.102  1.00  0.00           H  
ATOM     16  H   HYP A   1      -3.489   0.958   0.031  1.00  0.00           H  
CONECT    1    2   10                                                 
CONECT    2    1    3    6   11                                       
CONECT    3    2    4   12   13                                       
CONECT    4    3    5    7   14                                       
CONECT    5    4    6    6                                            
CONECT    6    5    5    2   15                                       
CONECT    7    4    8    9    9                                       
CONECT    8    7   16                                                 
CONECT    9    7    7                                                 
CONECT   10    1                                                      
CONECT   11    2                                                      
CONECT   12    3                                                      
CONECT   13    3                                                      
CONECT   14    4                                                      
CONECT   15    6                                                      
CONECT   16    8                                                      
MASTER        0    0    0    0    0    0    0    0   16    0   16    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Pyrroline hydroxycarboxylate	Generator
3-Hydroxy-L-1-pyrroline-5-carboxylate	HMDB
L-1-Pyrroline 3-hydroxy-5-carboxylate	HMDB
L-1-Pyrroline-3-hydroxy-5-carboxylate	HMDB
L-Delta1-Pyrroline 3-hydroxy-5-carboxylate	HMDB
Pyrroline-hydroxy-carboxylate	HMDB
3,4-Dihydro-3-hydroxy-2H-pyrrole-5-carboxylic acid	HMDB
3-Hydroxy delta 1-pyrroline-5-carboxylic acid	HMDB
3-Hydroxy delta 1-pyrroline-5-carboxylic acid, anion	HMDB

Chemical Formula

C₅H₇NO₃

Average Molecular Weight

129.114

Monoisotopic Molecular Weight

129.042593095

IUPAC Name

4-hydroxy-3,4-dihydro-2H-pyrrole-2-carboxylic acid

Traditional Name

pyrroline-hydroxy-carboxylate

CAS Registry Number

22573-88-2

SMILES

OC1CC(N=C1)C(O)=O

InChI Identifier

InChI=1S/C5H7NO3/c7-3-1-4(5(8)9)6-2-3/h2-4,7H,1H2,(H,8,9)

InChI Key

WFOFKRKDDKGRIK-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Pyrroline carboxylic acid
Pyrroline carboxylic acid or derivatives
Pyrroline
Secondary alcohol
Carboxylic acid
Monocarboxylic acid or derivatives
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Organoheterocyclic compound
Azacycle
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Organic oxide
Hydrocarbon derivative
Organic nitrogen compound
Carbonyl group
Alcohol
Imine
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

1-pyrrolinecarboxylic acid (CHEBI:27391 )

Ontology

Disposition

Source:

Endogenous

Biological location:

Biofluid and excreta:

Saliva

Subcellular:

Mitochondria

Process

Naturally occurring process:

Biological process:

Biochemical pathway:

Arginine and Proline Metabolism

Physical Properties

State

Solid

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

Predicted Molecular Properties

Property	Value	Source
Water Solubility	33.9 g/L	ALOGPS
logP	-1.1	ALOGPS
logP	-1.5	ChemAxon
logS	-0.58	ALOGPS
pKa (Strongest Acidic)	3.72	ChemAxon
pKa (Strongest Basic)	2.59	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	69.89 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	28.85 m³·mol⁻¹	ChemAxon
Polarizability	11.6 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Spectral Properties

Collision Cross Sections

Name	Adduct	Type	Data Source	Value	Reference
DarkChem	[M+H]+	Predicted	Not Available	127.351	31661259
DarkChem	[M-H]-	Predicted	Not Available	123.381	31661259
AllCCS	[M+H]+	Predicted	Not Available	128.809	32859911
AllCCS	[M-H]-	Predicted	Not Available	121.782	32859911

Retention Indices

Underivatized

Not Available

Derivatized

Derivative	Value	Reference
Pyrroline hydroxycarboxylic acid,1TMS,#1	1393.9111	https://arxiv.org/abs/1905.12712
Pyrroline hydroxycarboxylic acid,1TMS,#2	1277.0868	https://arxiv.org/abs/1905.12712
Pyrroline hydroxycarboxylic acid,2TMS,#1	1407.7148	https://arxiv.org/abs/1905.12712
Pyrroline hydroxycarboxylic acid,1TBDMS,#1	1640.6403	https://arxiv.org/abs/1905.12712
Pyrroline hydroxycarboxylic acid,1TBDMS,#2	1549.4475	https://arxiv.org/abs/1905.12712
Pyrroline hydroxycarboxylic acid,2TBDMS,#1	1839.3994	https://arxiv.org/abs/1905.12712

Spectra

GC-MS

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4l-9100000000-81454e4422185c7858e4	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0a4i-5910000000-0d5241ee660e7a60b0f9	2017-10-06	View Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-0006-9000000000-14721652508921574228	2021-09-05	View Spectrum

LC-MS/MS

Spectrum Type	Description	Splash Key	Deposition Date	View
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-001i-9600000000-8e7afe6ced148f01b715	2012-07-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-3900000000-91b528e579ac4acfac93	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-02u0-9400000000-c804fee192934438c532	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-014i-9000000000-7da85099ac98a08f5741	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-2900000000-ee7c942618fc6b2d94a9	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-02e9-9700000000-1d9848f227e64812ada6	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-015c-9000000000-0d2b20e1b4dbed83a144	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0900000000-06e1bd2d2793c5f0afaa	2021-09-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0059-9400000000-a84600f4fc13459b9448	2021-09-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-d2c2d7b1e05ce54b0932	2021-09-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-9300000000-c26ff3ebe1bb758e5252	2021-09-07	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-053r-9000000000-97da4a76921516901d46	2021-09-07	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0pc3-9000000000-8982b409276eceb00f1b	2021-09-07	View Spectrum

Biological Properties

Cellular Locations

Mitochondria

Biospecimen Locations

Saliva

Tissue Locations

Not Available

Pathways

Name	SMPDB/Pathwhiz	KEGG
Arginine and Proline Metabolism
Prolidase Deficiency (PD)		Not Available
Arginine: Glycine Amidinotransferase Deficiency (AGAT Deficiency)		Not Available
Hyperprolinemia Type II		Not Available
Hyperprolinemia Type I		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	20300169	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Oral cancer	20300169	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Female	Breast cancer	20300169	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Not Specified	Pancreatic cancer	20300169	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Not Specified	Periodontal diseases	20300169	details

Associated Disorders and Diseases

Disease References

Perillyl alcohol administration for cancer treatment
Sugimoto M, Wong DT, Hirayama A, Soga T, Tomita M: Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics. 2010 Mar;6(1):78-95. Epub 2009 Sep 10. [PubMed:20300169 ]
Pancreatic cancer
Sugimoto M, Wong DT, Hirayama A, Soga T, Tomita M: Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics. 2010 Mar;6(1):78-95. Epub 2009 Sep 10. [PubMed:20300169 ]
Periodontal disease
Sugimoto M, Wong DT, Hirayama A, Soga T, Tomita M: Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics. 2010 Mar;6(1):78-95. Epub 2009 Sep 10. [PubMed:20300169 ]

Associated OMIM IDs

260350 (Pancreatic cancer)
170650 (Periodontal disease)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022582

KNApSAcK ID

Not Available

Chemspider ID

1030

KEGG Compound ID

C04281

BioCyc ID

Not Available

BiGG ID

43511

Wikipedia Link

Not Available

METLIN ID

6196

PubChem Compound

1059

PDB ID

Not Available

ChEBI ID

27391

Food Biomarker Ontology

Not Available

VMH ID

1P3H5C

MarkerDB ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Simila S: Hydroxyproline metabolism in type II hyperprolinaemia. Ann Clin Biochem. 1979 Jul;16(4):177-81. [PubMed:533224 ]
Onenli-Mungan N, Yuksel B, Elkay M, Topaloglu AK, Baykal T, Ozer G: Type II hyperprolinemia: a case report. Turk J Pediatr. 2004 Apr-Jun;46(2):167-9. [PubMed:15214748 ]
Valle D, Goodman SI, Harris SC, Phang JM: Genetic evidence for a common enzyme catalyzing the second step in the degradation of proline and hydroxyproline. J Clin Invest. 1979 Nov;64(5):1365-70. [PubMed:500817 ]

Enzymes

Enzyme Details

1. Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial

General function:: Involved in oxidoreductase activity
Specific function:: Irreversible conversion of delta-1-pyrroline-5-carboxylate (P5C), derived either from proline or ornithine, to glutamate. This is a necessary step in the pathway interconnecting the urea and tricarboxylic acid cycles. The preferred substrate is glutamic gamma-semialdehyde, other substrates include succinic, glutaric and adipic semialdehydes.
Gene Name:: ALDH4A1
Uniprot ID:: P30038
Molecular weight:: 55117.24

Reactions

Pyrroline hydroxycarboxylic acid + NAD + Water → 4-Hydroxy-L-glutamic acid + NADH + Hydrogen Ion	details
Pyrroline hydroxycarboxylic acid + NADP + Water → 4-Hydroxy-L-glutamic acid + NADPH + Hydrogen Ion	details

Enzyme Details

2. Pyrroline-5-carboxylate reductase 1, mitochondrial

General function:: Involved in oxidoreductase activity
Specific function:: Housekeeping enzyme that catalyzes the last step in proline biosynthesis. Can utilize both NAD and NADP, but has higher affinity for NAD. Involved in the cellular response to oxidative stress.
Gene Name:: PYCR1
Uniprot ID:: P32322
Molecular weight:: 33360.27

Reactions

4-Hydroxyproline + NAD → Pyrroline hydroxycarboxylic acid + NADH + Hydrogen Ion	details
4-Hydroxyproline + NADP → Pyrroline hydroxycarboxylic acid + NADPH + Hydrogen Ion	details

Enzyme Details

3. Pyrroline-5-carboxylate reductase 2

General function:: Involved in oxidoreductase activity
Specific function:: Housekeeping enzyme that catalyzes the last step in proline biosynthesis. In some cell types, such as erythrocytes, its primary function may be the generation of NADP(+). Can utilize both NAD and NADP. Has higher affinity for NADP, but higher catalytic efficiency with NADH.
Gene Name:: PYCR2
Uniprot ID:: Q96C36
Molecular weight:: 25867.975

Reactions

4-Hydroxyproline + NAD → Pyrroline hydroxycarboxylic acid + NADH + Hydrogen Ion	details
4-Hydroxyproline + NADP → Pyrroline hydroxycarboxylic acid + NADPH + Hydrogen Ion	details

Enzyme Details

4. Pyrroline-5-carboxylate reductase 3

General function:: Involved in oxidoreductase activity
Specific function:: Not Available
Gene Name:: PYCRL
Uniprot ID:: Q53H96
Molecular weight:: 29892.415

Reactions

4-Hydroxyproline + NAD → Pyrroline hydroxycarboxylic acid + NADH + Hydrogen Ion	details
4-Hydroxyproline + NADP → Pyrroline hydroxycarboxylic acid + NADPH + Hydrogen Ion	details

Showing metabocard for Pyrroline hydroxycarboxylic acid (HMDB0001369)

MOL for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

3D MOL for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

3D SDF for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

3D-SDF for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

PDB for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

3D PDB for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

SMILES for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

INCHI for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

Structure for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

3D Structure for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

Collision Cross Sections

Retention Indices

Underivatized

Derivatized

GC-MS

LC-MS/MS

Enzymes

Reactions

Reactions

Reactions

Reactions