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Showing metabocard for Pyrroline hydroxycarboxylic acid (HMDB0001369)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:38:57 UTC
HMDB IDHMDB0001369
Secondary Accession Numbers
  • HMDB01369
Metabolite Identification
Common NamePyrroline hydroxycarboxylic acid
DescriptionPyrroline 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

  Mrv0541 02231219052D          

  9  9  0  0  0  0            999 V2000
   -0.2994    0.1099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2994   -0.7126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4093    0.5268    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0157    0.5192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1219   -0.7126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1219    0.1099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0157    1.3454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7283    0.1023    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7055   -1.2962    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  2  0  0  0  0
  4  7  1  0  0  0  0
  4  8  2  0  0  0  0
  5  9  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
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3D MOL for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

HMDB0001369
     RDKit          3D
Pyrroline hydroxycarboxylic acid
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.5616   -0.4281   -0.5805 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7284    0.0099    0.2582 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9488    1.2521    0.8497 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5606   -0.8335    0.5610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3144   -1.0430   -0.6865 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3151    0.0547   -0.4833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9102    1.2497   -1.0722 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3478    0.2257    0.9842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3192   -0.2658    1.5097 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2752    2.0247    0.2844 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9067   -1.8228    0.9623 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7371   -2.0422   -0.6006 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3373   -0.8948   -1.5723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3221   -0.1963   -0.8717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8572    1.9767   -0.4106 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1954    0.7331    1.5280 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  9  4  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
M  END
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3D SDF for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

  Mrv0541 02231219052D          

  9  9  0  0  0  0            999 V2000
   -0.2994    0.1099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2994   -0.7126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4093    0.5268    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0157    0.5192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1219   -0.7126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1219    0.1099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0157    1.3454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7283    0.1023    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7055   -1.2962    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  2  0  0  0  0
  4  7  1  0  0  0  0
  4  8  2  0  0  0  0
  5  9  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001369

> <DATABASE_NAME>
hmdb

> <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

> <FORMULA>
C5H7NO3

> <MOLECULAR_WEIGHT>
129.114

> <EXACT_MASS>
129.042593095

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
11.595062277388251

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-hydroxy-3,4-dihydro-2H-pyrrole-2-carboxylic acid

> <ALOGPS_LOGP>
-1.10

> <JCHEM_LOGP>
-1.4545071951925133

> <ALOGPS_LOGS>
-0.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.25483703022578

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7212230695209163

> <JCHEM_PKA_STRONGEST_BASIC>
2.5899435587205386

> <JCHEM_POLAR_SURFACE_AREA>
69.89

> <JCHEM_REFRACTIVITY>
28.8459

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.39e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrroline-hydroxy-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

HMDB0001369
     RDKit          3D
Pyrroline hydroxycarboxylic acid
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.5616   -0.4281   -0.5805 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7284    0.0099    0.2582 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9488    1.2521    0.8497 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5606   -0.8335    0.5610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3144   -1.0430   -0.6865 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3151    0.0547   -0.4833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9102    1.2497   -1.0722 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3478    0.2257    0.9842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3192   -0.2658    1.5097 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2752    2.0247    0.2844 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9067   -1.8228    0.9623 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7371   -2.0422   -0.6006 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3373   -0.8948   -1.5723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3221   -0.1963   -0.8717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8572    1.9767   -0.4106 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1954    0.7331    1.5280 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  9  4  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
M  END
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PDB for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      -0.559   0.205   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.559  -1.330   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       0.764   0.983   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -1.896   0.969   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.094  -1.330   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.094   0.205   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.896   2.511   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -3.226   0.191   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       3.184  -2.420   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    1    7    8                                                  
CONECT    5    2    9    6                                                  
CONECT    6    3    5                                                       
CONECT    7    4                                                            
CONECT    8    4                                                            
CONECT    9    5                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

COMPND    HMDB0001369
HETATM    1  O1  UNL     1       2.562  -0.428  -0.580  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.728   0.010   0.258  1.00  0.00           C  
HETATM    3  O2  UNL     1       1.949   1.252   0.850  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.561  -0.834   0.561  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.314  -1.043  -0.687  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.315   0.055  -0.483  1.00  0.00           C  
HETATM    7  O3  UNL     1      -0.910   1.250  -1.072  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.348   0.226   0.984  1.00  0.00           C  
HETATM    9  N1  UNL     1      -0.319  -0.266   1.510  1.00  0.00           N  
HETATM   10  H1  UNL     1       2.275   2.025   0.284  1.00  0.00           H  
HETATM   11  H2  UNL     1       0.907  -1.823   0.962  1.00  0.00           H  
HETATM   12  H3  UNL     1      -0.737  -2.042  -0.601  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.337  -0.895  -1.572  1.00  0.00           H  
HETATM   14  H5  UNL     1      -2.322  -0.196  -0.872  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.857   1.977  -0.411  1.00  0.00           H  
HETATM   16  H7  UNL     1      -2.195   0.733   1.528  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   10
CONECT    4    5    9   11
CONECT    5    6   12   13
CONECT    6    7    8   14
CONECT    7   15
CONECT    8    9    9   16
END
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SMILES for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

OC1CC(N=C1)C(O)=O
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INCHI for HMDB0001369 (Pyrroline hydroxycarboxylic acid)

InChI=1S/C5H7NO3/c7-3-1-4(5(8)9)6-2-3/h2-4,7H,1H2,(H,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Pyrroline hydroxycarboxylateGenerator
3-Hydroxy-L-1-pyrroline-5-carboxylateHMDB
L-1-Pyrroline 3-hydroxy-5-carboxylateHMDB
L-1-Pyrroline-3-hydroxy-5-carboxylateHMDB
L-Delta1-Pyrroline 3-hydroxy-5-carboxylateHMDB
Pyrroline-hydroxy-carboxylateHMDB
3,4-Dihydro-3-hydroxy-2H-pyrrole-5-carboxylic acidHMDB
3-Hydroxy delta 1-pyrroline-5-carboxylic acidHMDB
3-Hydroxy delta 1-pyrroline-5-carboxylic acid, anionHMDB
Chemical FormulaC5H7NO3
Average Molecular Weight129.114
Monoisotopic Molecular Weight129.042593095
IUPAC Name4-hydroxy-3,4-dihydro-2H-pyrrole-2-carboxylic acid
Traditional Namepyrroline-hydroxy-carboxylate
CAS Registry Number22573-88-2
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 KeyWFOFKRKDDKGRIK-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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha 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 FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Mitochondria
Biospecimen Locations
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothOral cancer details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)FemaleBreast cancer details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not SpecifiedPancreatic cancer details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not SpecifiedPeriodontal diseases details
Associated Disorders and Diseases
Disease References
Perillyl alcohol administration for cancer treatment
  1. 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
  1. 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
  1. 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
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022582
KNApSAcK IDNot Available
Chemspider ID1030
KEGG Compound IDC04281
BioCyc IDNot Available
BiGG ID43511
Wikipedia LinkNot Available
METLIN ID6196
PubChem Compound1059
PDB IDNot Available
ChEBI ID27391
Food Biomarker OntologyNot Available
VMH ID1P3H5C
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simila S: Hydroxyproline metabolism in type II hyperprolinaemia. Ann Clin Biochem. 1979 Jul;16(4):177-81. [PubMed:533224 ]
  2. 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 ]
  3. 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 Iondetails
Pyrroline hydroxycarboxylic acid + NADP + Water → 4-Hydroxy-L-glutamic acid + NADPH + Hydrogen Iondetails
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 Iondetails
4-Hydroxyproline + NADP → Pyrroline hydroxycarboxylic acid + NADPH + Hydrogen Iondetails
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 Iondetails
4-Hydroxyproline + NADP → Pyrroline hydroxycarboxylic acid + NADPH + Hydrogen Iondetails
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 Iondetails
4-Hydroxyproline + NADP → Pyrroline hydroxycarboxylic acid + NADPH + Hydrogen Iondetails