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Showing metabocard for 1-Pyrroline-2-carboxylic acid (HMDB0006875)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2008-08-13 17:53:39 UTC
Update Date2023-02-21 17:17:22 UTC
HMDB IDHMDB0006875
Secondary Accession Numbers
  • HMDB06875
Metabolite Identification
Common Name1-Pyrroline-2-carboxylic acid
Description1-Pyrroline-2-carboxylic acid, also known as delta1-pyrroline 2-carboxylate, belongs to the class of organic compounds known as pyrrolines. Pyrrolines are compounds containing a pyrroline ring, which is a five-member unsaturated aliphatic ring with one nitrogen atom and four carbon atoms. 1-Pyrroline-2-carboxylic acid is a moderately basic compound (based on its pKa). 1-Pyrroline-2-carboxylic acid exists in all living organisms, ranging from bacteria to humans. 1-pyrroline-2-carboxylic acid can be biosynthesized from D-proline through its interaction with the enzyme D-amino-acid oxidase. The product resulting from formal oxidation of DL-proline by loss of hydrogen from the nitrogen and from the carbon alpha to the carboxylic acid, with the formation of a C=N bond. In humans, 1-pyrroline-2-carboxylic acid is involved in the metabolic disorder called hyperprolinemia type II.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0006875 (1-Pyrroline-2-carboxylic acid)

  Mrv1652309152018192D          

  8  8  0  0  0  0            999 V2000
10000.682310000.1792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.3973 9999.7677    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.682310001.0035    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.297510000.2623    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6301 9999.7773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.8850 9998.9927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.7100 9998.9927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.9649 9999.7773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  5  1  0  0  0  0
  4  8  2  0  0  0  0
  1  8  1  0  0  0  0
M  END
Download

3D MOL for HMDB0006875 (1-Pyrroline-2-carboxylic acid)

HMDB0006875
     RDKit          3D
1-Pyrroline-2-carboxylic acid
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.4854   -1.8375    0.4795 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0006   -0.7758    0.0164 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8879    0.1635   -0.4847 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5615   -0.5197   -0.0036 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3554   -1.3317    0.4400 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6728   -0.7543    0.2613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3338    0.7410    0.3289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0850    0.7115   -0.5348 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8295    1.0951   -0.0601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3822   -1.0451    1.0527 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0135   -0.9494   -0.7559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9918    1.0170    1.3529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1261    1.3627   -0.0667 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5379    1.6100   -0.4170 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3420    0.5127   -1.6088 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  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  4  1  0
  3  9  1  0
  6 10  1  0
  6 11  1  0
  7 12  1  0
  7 13  1  0
  8 14  1  0
  8 15  1  0
M  END
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3D SDF for HMDB0006875 (1-Pyrroline-2-carboxylic acid)

  Mrv1652309152018192D          

  8  8  0  0  0  0            999 V2000
10000.682310000.1792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.3973 9999.7677    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.682310001.0035    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.297510000.2623    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6301 9999.7773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.8850 9998.9927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.7100 9998.9927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.9649 9999.7773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  5  1  0  0  0  0
  4  8  2  0  0  0  0
  1  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0006875

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C1=NCCC1

> <INCHI_IDENTIFIER>
InChI=1S/C5H7NO2/c7-5(8)4-2-1-3-6-4/h1-3H2,(H,7,8)

> <INCHI_KEY>
RHTAIKJZSXNELN-UHFFFAOYSA-N

> <FORMULA>
C5H7NO2

> <MOLECULAR_WEIGHT>
113.1146

> <EXACT_MASS>
113.047678473

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.81138734712021

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4-dihydro-2H-pyrrol-1-ium-5-carboxylate

> <ALOGPS_LOGP>
0.25

> <JCHEM_LOGP>
0.5292144963333332

> <ALOGPS_LOGS>
-1.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9331828370415765

> <JCHEM_PKA_STRONGEST_BASIC>
1.7241099274971199

> <JCHEM_POLAR_SURFACE_AREA>
54.099999999999994

> <JCHEM_REFRACTIVITY>
49.890800000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.26e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,5-dihydro-3H-pyrrol-1-ium-2-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0006875 (1-Pyrroline-2-carboxylic acid)

HMDB0006875
     RDKit          3D
1-Pyrroline-2-carboxylic acid
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.4854   -1.8375    0.4795 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0006   -0.7758    0.0164 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8879    0.1635   -0.4847 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5615   -0.5197   -0.0036 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3554   -1.3317    0.4400 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6728   -0.7543    0.2613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3338    0.7410    0.3289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0850    0.7115   -0.5348 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8295    1.0951   -0.0601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3822   -1.0451    1.0527 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0135   -0.9494   -0.7559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9918    1.0170    1.3529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1261    1.3627   -0.0667 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5379    1.6100   -0.4170 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3420    0.5127   -1.6088 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  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  4  1  0
  3  9  1  0
  6 10  1  0
  6 11  1  0
  7 12  1  0
  7 13  1  0
  8 14  1  0
  8 15  1  0
M  END
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PDB for HMDB0006875 (1-Pyrroline-2-carboxylic acid)

HEADER    PROTEIN                                 15-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-SEP-20         0                                  
HETATM    1  C   UNK     0    8667.9408667.001   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8669.2758666.233   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8667.9408668.540   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0    8665.3558667.156   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0    8664.1108666.251   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8664.5858664.786   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8666.1258664.786   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8666.6018666.251   0.000  0.00  0.00           C+0
CONECT    1    2    3    8                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    5    8                                                       
CONECT    5    6    4                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    4    1                                                  
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0006875 (1-Pyrroline-2-carboxylic acid)

COMPND    HMDB0006875
HETATM    1  O1  UNL     1       2.485  -1.838   0.479  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.001  -0.776   0.016  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.888   0.164  -0.485  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.561  -0.520  -0.004  1.00  0.00           C  
HETATM    5  N1  UNL     1      -0.355  -1.332   0.440  1.00  0.00           N  
HETATM    6  C3  UNL     1      -1.673  -0.754   0.261  1.00  0.00           C  
HETATM    7  C4  UNL     1      -1.334   0.741   0.329  1.00  0.00           C  
HETATM    8  C5  UNL     1      -0.085   0.712  -0.535  1.00  0.00           C  
HETATM    9  H1  UNL     1       2.829   1.095  -0.060  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.382  -1.045   1.053  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.013  -0.949  -0.756  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.992   1.017   1.353  1.00  0.00           H  
HETATM   13  H5  UNL     1      -2.126   1.363  -0.067  1.00  0.00           H  
HETATM   14  H6  UNL     1       0.538   1.610  -0.417  1.00  0.00           H  
HETATM   15  H7  UNL     1      -0.342   0.513  -1.609  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    9
CONECT    4    5    5    8
CONECT    5    6
CONECT    6    7   10   11
CONECT    7    8   12   13
CONECT    8   14   15
END
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SMILES for HMDB0006875 (1-Pyrroline-2-carboxylic acid)

OC(=O)C1=NCCC1
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INCHI for HMDB0006875 (1-Pyrroline-2-carboxylic acid)

InChI=1S/C5H7NO2/c7-5(8)4-2-1-3-6-4/h1-3H2,(H,7,8)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1-Pyrroline-2-carboxylateChEBI
delta1-Pyrroline 2-carboxylateChEBI
1-Pyrroline 2-carboxylateKegg
delta1-Pyrroline 2-carboxylic acidGenerator
Δ1-pyrroline 2-carboxylateGenerator
Δ1-pyrroline 2-carboxylic acidGenerator
1-Pyrroline 2-carboxylic acidGenerator
3,4-Dihydro-2H-pyrrole-5-carboxylateHMDB
3,4-Dihydro-2H-pyrrole-5-carboxylic acidHMDB
D1-Pyrroline 2-carboxylateHMDB
D1-Pyrroline 2-carboxylic acidHMDB
delta-1-Pyrroline-2-carboxylateHMDB
1,2-DidehydroprolineHMDB
1-Pyrroline-2-carboxylic acidHMDB
delta1-Pyrroline-2-carboxylic acidHMDB
Δ1-Pyrroline-2-carboxylic acidHMDB
Chemical FormulaC5H7NO2
Average Molecular Weight113.1146
Monoisotopic Molecular Weight113.047678473
IUPAC Name3,4-dihydro-2H-pyrrol-1-ium-5-carboxylate
Traditional Name4,5-dihydro-3H-pyrrol-1-ium-2-carboxylate
CAS Registry Number2139-03-9
SMILES
OC(=O)C1=NCCC1
InChI Identifier
InChI=1S/C5H7NO2/c7-5(8)4-2-1-3-6-4/h1-3H2,(H,7,8)
InChI KeyRHTAIKJZSXNELN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolines. Pyrrolines are compounds containing a pyrroline ring, which is a five-member unsaturated aliphatic ring with one nitrogen atom and four carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyrrolines
Sub ClassNot Available
Direct ParentPyrrolines
Alternative Parents
Substituents
  • Pyrroline
  • Ketimine
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Imine
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
Role
Industrial application
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 LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB02838
Phenol Explorer Compound IDNot Available
FooDB IDFDB024129
KNApSAcK IDNot Available
Chemspider ID389057
KEGG Compound IDC03564
BioCyc IDDELTA1-PYRROLINE_2-CARBOXYLATE
BiGG ID42087
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound440046
PDB ID2PC
ChEBI ID36761
Food Biomarker OntologyNot Available
VMH ID1P2CBXL
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. D-amino-acid oxidase
General function:
Involved in D-amino-acid oxidase activity
Specific function:
Regulates the level of the neuromodulator D-serine in the brain. Has high activity towards D-DOPA and contributes to dopamine synthesis. Could act as a detoxifying agent which removes D-amino acids accumulated during aging. Acts on a variety of D-amino acids with a preference for those having small hydrophobic side chains followed by those bearing polar, aromatic, and basic groups. Does not act on acidic amino acids.
Gene Name:
DAO
Uniprot ID:
P14920
Molecular weight:
39473.75
Reactions
D-Proline + Oxygen → 1-Pyrroline-2-carboxylic acid + Hydrogen peroxidedetails