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Showing metabocard for DL-Proline (HMDB0251528)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 08:53:28 UTC
Update Date2021-09-26 23:03:34 UTC
HMDB IDHMDB0251528
Secondary Accession NumbersNone
Metabolite Identification
Common NameDL-Proline
DescriptionProline, also known as DL-proline or hpro, belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. In humans, proline is involved in the metabolic disorder called hyperornithinemia with gyrate atrophy (hoga). Proline is found, on average, in the highest concentration within a few different foods, such as milk (cow), wheats (Triticum), and oats (Avena sativa) and in a lower concentration in winter squashes (Cucurbita maxima), pacific jack mackerels (Trachurus symmetricus), and coconuts (Cocos nucifera). Proline has also been detected, but not quantified in, several different foods, such as sunflower oil, rapeseed oil, tallow, soybean oil, and vodka. This could make proline a potential biomarker for the consumption of these foods. Proline is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Proline. This compound has been identified in human blood as reported by (PMID: 31557052 ). Dl-proline is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically DL-Proline is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0251528 (DL-Proline)

  Mrv0541 09041212432D          

  8  8  0  0  0  0            999 V2000
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  4  1  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  2  0  0  0  0
  8  5  1  0  0  0  0
M  END
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3D MOL for HMDB0251528 (DL-Proline)

HMDB0251528
     RDKit          3D
DL-Proline
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.7977   -1.1894    0.1754 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9672   -0.4111    0.3266 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2632    0.7882    1.0789 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5682   -0.4522   -0.2193 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4254   -0.7178    0.8245 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6842   -0.3369   -0.0094 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1307    0.9968   -0.5044 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1991    0.6535   -0.9706 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5182    1.5842    0.4611 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5583   -1.3428   -0.9299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3933   -0.0381    1.6697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5095   -1.8143    1.1528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6589   -1.0572   -0.8492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5940   -0.3037    0.5708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7421    1.4681   -1.2396 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9803    1.6196    0.4117 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2468    0.5531   -1.9492 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
  7  8  1  0
  8  4  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
  7 16  1  0
  8 17  1  0
M  END
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3D SDF for HMDB0251528 (DL-Proline)

  Mrv0541 09041212432D          

  8  8  0  0  0  0            999 V2000
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  4  1  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  2  0  0  0  0
  8  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0251528

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C1CCCN1

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)

> <INCHI_KEY>
ONIBWKKTOPOVIA-UHFFFAOYSA-N

> <FORMULA>
C5H9NO2

> <MOLECULAR_WEIGHT>
115.1305

> <EXACT_MASS>
115.063328537

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
11.536467742937543

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyrrolidine-2-carboxylic acid

> <ALOGPS_LOGP>
-2.71

> <JCHEM_LOGP>
-2.568638276039985

> <ALOGPS_LOGS>
0.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.9406707712827895

> <JCHEM_PKA_STRONGEST_BASIC>
11.332026115136207

> <JCHEM_POLAR_SURFACE_AREA>
49.33

> <JCHEM_REFRACTIVITY>
28.064300000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.65e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
proline

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0251528 (DL-Proline)

HMDB0251528
     RDKit          3D
DL-Proline
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.7977   -1.1894    0.1754 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9672   -0.4111    0.3266 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2632    0.7882    1.0789 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5682   -0.4522   -0.2193 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4254   -0.7178    0.8245 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6842   -0.3369   -0.0094 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1307    0.9968   -0.5044 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1991    0.6535   -0.9706 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5182    1.5842    0.4611 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5583   -1.3428   -0.9299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3933   -0.0381    1.6697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5095   -1.8143    1.1528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6589   -1.0572   -0.8492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5940   -0.3037    0.5708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7421    1.4681   -1.2396 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9803    1.6196    0.4117 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2468    0.5531   -1.9492 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
  7  8  1  0
  8  4  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
  7 16  1  0
  8 17  1  0
M  END
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PDB for HMDB0251528 (DL-Proline)

HEADER    PROTEIN                                 04-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    6                                                       
CONECT    4    2    5    6                                                  
CONECT    5    4    7    8                                                  
CONECT    6    3    4                                                       
CONECT    7    5                                                            
CONECT    8    5                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0251528 (DL-Proline)

COMPND    HMDB0251528
HETATM    1  O1  UNL     1       2.798  -1.189   0.175  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.967  -0.411   0.327  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.263   0.788   1.079  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.568  -0.452  -0.219  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.425  -0.718   0.825  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.684  -0.337  -0.009  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.131   0.997  -0.504  1.00  0.00           C  
HETATM    8  N1  UNL     1       0.199   0.654  -0.971  1.00  0.00           N  
HETATM    9  H1  UNL     1       2.518   1.584   0.461  1.00  0.00           H  
HETATM   10  H2  UNL     1       0.558  -1.343  -0.930  1.00  0.00           H  
HETATM   11  H3  UNL     1      -0.393  -0.038   1.670  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.510  -1.814   1.153  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.659  -1.057  -0.849  1.00  0.00           H  
HETATM   14  H6  UNL     1      -2.594  -0.304   0.571  1.00  0.00           H  
HETATM   15  H7  UNL     1      -1.742   1.468  -1.240  1.00  0.00           H  
HETATM   16  H8  UNL     1      -0.980   1.620   0.412  1.00  0.00           H  
HETATM   17  H9  UNL     1       0.247   0.553  -1.949  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    9
CONECT    4    5    8   10
CONECT    5    6   11   12
CONECT    6    7   13   14
CONECT    7    8   15   16
CONECT    8   17
END
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SMILES for HMDB0251528 (DL-Proline)

OC(=O)C1CCCN1
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INCHI for HMDB0251528 (DL-Proline)

InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
DL-ProlineChEBI
HproChEBI
ProlinChEBI
ProlinaChEBI
Pyrrolidine-2-carboxylic acidChEBI
Pyrrolidine-2-carboxylateGenerator
L-ProlineMeSH
L ProlineMeSH
Chemical FormulaC5H9NO2
Average Molecular Weight115.1305
Monoisotopic Molecular Weight115.063328537
IUPAC Namepyrrolidine-2-carboxylic acid
Traditional Nameproline
CAS Registry NumberNot Available
SMILES
OC(=O)C1CCCN1
InChI Identifier
InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)
InChI KeyONIBWKKTOPOVIA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentProline and derivatives
Alternative Parents
Substituents
  • Proline or derivatives
  • Alpha-amino acid
  • Pyrrolidine carboxylic acid
  • Pyrrolidine carboxylic acid or derivatives
  • Pyrrolidine
  • Amino acid
  • Azacycle
  • Organoheterocyclic compound
  • Secondary amine
  • Monocarboxylic acid or derivatives
  • Secondary aliphatic amine
  • Carboxylic acid
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Amine
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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 Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030009
KNApSAcK IDC00001345
Chemspider ID594
KEGG Compound IDC16435
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkProline
METLIN IDNot Available
PubChem Compound614
PDB IDNot Available
ChEBI ID26271
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1242001
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]