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Showing metabocard for Pyrrole-2-carboxylic acid (HMDB0004230)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-08-13 14:52:55 UTC
Update Date2023-02-21 17:16:58 UTC
HMDB IDHMDB0004230
Secondary Accession Numbers
  • HMDB0003094
  • HMDB03094
  • HMDB04230
Metabolite Identification
Common NamePyrrole-2-carboxylic acid
DescriptionPyrrole-2-carboxylic acid was synthesized over a century ago, but its history as a compound of biological origin is rather recent. It was first identified as a degradation product of sialic acids, then as a derivative of the oxidation of the D-hydroxyproline isomers by mammalian D-amino acid oxidase. The latter relationship results from the lability of the direct oxidation product, A'-pyrroline-4-hydroxy-2-carboxylic acid, which loses water spontaneously to form the pyrrole. A similar reaction is catalyzed by the more specific allohydroxy-D-proline oxidase of Pseudomonas. In whole animal observations, pyrrole-2-carboxylate (PCA) ' was identified in rat or human urine after administration of the D-isomers of hydroxyproline, a finding ascribable to the action of D-amino acid oxidase. (PMID:4430715 ). Urinary excretion of N-(pyrrole-2-carboxyl) glycine has been reported in a 5-year-old affected with type II hyperprolinemia; The child has mild developmental delay, recurrent seizures of the grand mal type and EEG alterations. The urinary excretion of the conjugate is stressed, since it appears that only one previous report in the literature described this compound in the urine of two patients affected by this disturbance (PMID 2383933 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0004230 (Pyrrole-2-carboxylic acid)

  Mrv1652305271900282D          

  8  8  0  0  0  0            999 V2000
   35.3109  -24.7215    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   34.8694  -26.0806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   33.2457  -25.5036    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   33.9131  -25.0186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   33.6582  -24.2340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   32.5782  -25.0186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   32.8331  -24.2340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   34.6978  -25.2736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  8  2  0  0  0  0
  3  4  1  0  0  0  0
  3  6  1  0  0  0  0
  4  5  2  0  0  0  0
  4  8  1  0  0  0  0
  5  7  1  0  0  0  0
  6  7  2  0  0  0  0
M  END
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3D MOL for HMDB0004230 (Pyrrole-2-carboxylic acid)

HMDB0004230
     RDKit          3D
Pyrrole-2-carboxylic acid
 13 13  0  0  0  0  0  0  0  0999 V2000
    2.2849    1.3720   -0.6393 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7747    0.2701   -0.3807 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5814   -0.8539   -0.3182 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3475    0.1345   -0.1418 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5845    1.1774   -0.1719 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8415    0.6808    0.1005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6686   -0.6737    0.2970 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3654   -0.9556    0.1456 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9277   -1.2262    0.5612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3508    2.2073   -0.3767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7938    1.2151    0.1571 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4064   -1.4380    0.5346 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0947   -1.9097    0.2326 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  2  0
  7  8  1  0
  8  4  1  0
  3  9  1  0
  5 10  1  0
  6 11  1  0
  7 12  1  0
  8 13  1  0
M  END
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3D SDF for HMDB0004230 (Pyrrole-2-carboxylic acid)

  Mrv1652305271900282D          

  8  8  0  0  0  0            999 V2000
   35.3109  -24.7215    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   34.8694  -26.0806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   33.2457  -25.5036    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   33.9131  -25.0186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   33.6582  -24.2340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   32.5782  -25.0186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   32.8331  -24.2340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   34.6978  -25.2736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  8  2  0  0  0  0
  3  4  1  0  0  0  0
  3  6  1  0  0  0  0
  4  5  2  0  0  0  0
  4  8  1  0  0  0  0
  5  7  1  0  0  0  0
  6  7  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0004230

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C1=CC=CN1

> <INCHI_IDENTIFIER>
InChI=1S/C5H5NO2/c7-5(8)4-2-1-3-6-4/h1-3,6H,(H,7,8)

> <INCHI_KEY>
WRHZVMBBRYBTKZ-UHFFFAOYSA-N

> <FORMULA>
C5H5NO2

> <MOLECULAR_WEIGHT>
111.0987

> <EXACT_MASS>
111.032028409

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
10.236333320971507

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1H-pyrrole-2-carboxylic acid

> <ALOGPS_LOGP>
0.70

> <JCHEM_LOGP>
0.6307139603333332

> <ALOGPS_LOGS>
0.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
17.17399398326462

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.16397234010439

> <JCHEM_POLAR_SURFACE_AREA>
53.089999999999996

> <JCHEM_REFRACTIVITY>
27.9505

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.64e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
minalin

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0004230 (Pyrrole-2-carboxylic acid)

HMDB0004230
     RDKit          3D
Pyrrole-2-carboxylic acid
 13 13  0  0  0  0  0  0  0  0999 V2000
    2.2849    1.3720   -0.6393 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7747    0.2701   -0.3807 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5814   -0.8539   -0.3182 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3475    0.1345   -0.1418 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5845    1.1774   -0.1719 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8415    0.6808    0.1005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6686   -0.6737    0.2970 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3654   -0.9556    0.1456 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9277   -1.2262    0.5612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3508    2.2073   -0.3767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7938    1.2151    0.1571 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4064   -1.4380    0.5346 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0947   -1.9097    0.2326 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  2  0
  7  8  1  0
  8  4  1  0
  3  9  1  0
  5 10  1  0
  6 11  1  0
  7 12  1  0
  8 13  1  0
M  END
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PDB for HMDB0004230 (Pyrrole-2-carboxylic acid)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0      65.914 -46.147   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      65.090 -48.684   0.000  0.00  0.00           O+0
HETATM    3  N   UNK     0      62.059 -47.607   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      63.304 -46.701   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      62.829 -45.237   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      60.813 -46.701   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      61.288 -45.237   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      64.769 -47.177   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2    8                                                            
CONECT    3    4    6                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    7                                                       
CONECT    6    3    7                                                       
CONECT    7    5    6                                                       
CONECT    8    1    2    4                                                  
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0004230 (Pyrrole-2-carboxylic acid)

COMPND    HMDB0004230
HETATM    1  O1  UNL     1       2.285   1.372  -0.639  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.775   0.270  -0.381  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.581  -0.854  -0.318  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.347   0.134  -0.142  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.584   1.177  -0.172  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.841   0.681   0.100  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.669  -0.674   0.297  1.00  0.00           C  
HETATM    8  N1  UNL     1      -0.365  -0.956   0.146  1.00  0.00           N  
HETATM    9  H1  UNL     1       2.928  -1.226   0.561  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.351   2.207  -0.377  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.794   1.215   0.157  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.406  -1.438   0.535  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.095  -1.910   0.233  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    9
CONECT    4    5    5    8
CONECT    5    6   10
CONECT    6    7    7   11
CONECT    7    8   12
CONECT    8   13
END
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SMILES for HMDB0004230 (Pyrrole-2-carboxylic acid)

OC(=O)C1=CC=CN1
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INCHI for HMDB0004230 (Pyrrole-2-carboxylic acid)

InChI=1S/C5H5NO2/c7-5(8)4-2-1-3-6-4/h1-3,6H,(H,7,8)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Pyrrolecarboxylic acidChEBI
MinalineChEBI
PCAChEBI
Pyrrole-2-carboxylateChEBI
2-PyrrolecarboxylateGenerator
1H-Pyrrole-2-carboxylic acidHMDB
1H-Pyrrole-2-carboxylic acid (9ci)HMDB
2-MinalineHMDB
MinalinHMDB
PYCHMDB
2-Pyrrolecarboxylic acid, monosodium saltMeSH, HMDB
Pyrrole-2-carboxylic acidGenerator
Chemical FormulaC5H5NO2
Average Molecular Weight111.0987
Monoisotopic Molecular Weight111.032028409
IUPAC Name1H-pyrrole-2-carboxylic acid
Traditional Nameminalin
CAS Registry Number634-97-9
SMILES
OC(=O)C1=CC=CN1
InChI Identifier
InChI=1S/C5H5NO2/c7-5(8)4-2-1-3-6-4/h1-3,6H,(H,7,8)
InChI KeyWRHZVMBBRYBTKZ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrole 2-carboxylic acids. These are pyrrole carboxylic acids where the carboxyl group is attached at position C2.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyrroles
Sub ClassPyrrole carboxylic acids and derivatives
Direct ParentPyrrole 2-carboxylic acids
Alternative Parents
Substituents
  • Pyrrole-2-carboxylic acid
  • Substituted pyrrole
  • Heteroaromatic compound
  • Azacycle
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
Role
Industrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP0.85POMONA (1987)
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Not Available114.8http://allccs.zhulab.cn/database/detail?ID=AllCCS00002133
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified0.03 +/- 0.02 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB02543
Phenol Explorer Compound IDNot Available
FooDB IDFDB023340
KNApSAcK IDC00043859
Chemspider ID11963
KEGG Compound IDC05942
BioCyc IDCPD-478
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID3787
PubChem Compound12473
PDB IDNot Available
ChEBI ID36751
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceKosugi, Yoshio. Pyrrole-2-carboxylic acids and manufacturing methods therefor. Jpn. Kokai Tokkyo Koho (2002), 5 pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Wajner M, Wannmacher CM, Purkiss P: High urinary excretion of N-(pyrrole-2-carboxyl) glycine in type II hyperprolinemia. Clin Genet. 1990 Jun;37(6):485-9. [PubMed:2383933 ]
  2. Heacock AM, Adams E: Formation and excretion of pyrrole-2-carboxylic acid. Whole animal and enzyme studies in the rat. J Biol Chem. 1975 Apr 10;250(7):2599-608. [PubMed:235519 ]
  3. Heacock AM, Adams E: Formation and excretion of pyrrole-2-carboxylate in man. J Clin Invest. 1974 Oct;54(4):810-8. [PubMed:4430715 ]