Showing metabocard for Proline betaine (MMDBc0000606)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:50:58 UTC
Update Date2024-10-13 13:49:51 UTC
Metabolite IDMMDBc0000606
Metabolite Identification
Common NameProline betaine
DescriptionProline betaine is an osmoprotective compound found in urine. It is thought to serve an osmoprotective role for the kidney. Proline betaine is a glycine betaine analogue found in many citrus foods. Elevated levels of proline betaine in human urine are found after the consumption of citrus fruits and juices (PMID: 18060588 ). Proline betaine is a biomarker for the consumption of citrus fruits.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f46d431b8a8>


  Mrv1652309121709222D          

 10 10  0  0  1  0            999 V2000
    0.0157    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 N   0  3  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
    0.9803   -0.1553    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
   -0.0997    0.6294    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.1198    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  2 10  1  0  0  0  0
M  CHG  2   2   1   9  -1
M  END
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3D MOL for #<Metabolite:0x00007f46d431b8a8>

HMDB0004827
     RDKit          3D
Proline betaine
 23 23  0  0  0  0  0  0  0  0999 V2000
   -1.4735    0.5232    1.2093 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5708    0.1635    0.1513 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.9665    0.7333   -1.0917 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6455   -1.2998    0.0151 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5994   -1.6346   -0.7598 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6172   -0.6865   -0.1744 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7804    0.3567    0.5328 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3273    1.6941    0.3295 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8264    2.6134   -0.3634 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5265    1.9944    0.9629 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.1698   -0.0223    2.1197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4650    1.6234    1.3503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5068    0.2500    0.8707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9056    0.1927   -1.4140 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2396    0.5733   -1.8940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2566    1.7997   -1.0445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5548   -1.6187   -0.5012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5505   -1.7266    1.0303 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8511   -2.6892   -0.6083 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4745   -1.4549   -1.8541 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1901   -0.2366   -1.0150 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2500   -1.2714    0.5180 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8623    0.1229    1.6306 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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  9  2  0
  8 10  1  0
  7  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  1
M  CHG  2   2   1  10  -1
M  END
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3D SDF for #<Metabolite:0x00007f46d431b8a8>


  Mrv1652309121709222D          

 10 10  0  0  1  0            999 V2000
    0.0157    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 N   0  3  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
    0.9803   -0.1553    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
   -0.0997    0.6294    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.1198    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  2 10  1  0  0  0  0
M  CHG  2   2   1   9  -1
M  END
> <DATABASE_ID>
MMDBc0000606

> <DATABASE_NAME>
MIME

> <SMILES>
C[N+]1(C)CCC[C@H]1C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H13NO2/c1-8(2)5-3-4-6(8)7(9)10/h6H,3-5H2,1-2H3/t6-/m0/s1

> <INCHI_KEY>
CMUNUTVVOOHQPW-LURJTMIESA-N

> <FORMULA>
C7H13NO2

> <MOLECULAR_WEIGHT>
143.1836

> <EXACT_MASS>
143.094628665

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.05016181177956

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-1,1-dimethylpyrrolidin-1-ium-2-carboxylate

> <ALOGPS_LOGP>
-2.24

> <JCHEM_LOGP>
-3.8764300881384117

> <ALOGPS_LOGS>
-2.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.258526077274334

> <JCHEM_POLAR_SURFACE_AREA>
40.129999999999995

> <JCHEM_REFRACTIVITY>
60.10970000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.66e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
stachydrine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f46d431b8a8>

HMDB0004827
     RDKit          3D
Proline betaine
 23 23  0  0  0  0  0  0  0  0999 V2000
   -1.4735    0.5232    1.2093 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5708    0.1635    0.1513 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.9665    0.7333   -1.0917 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6455   -1.2998    0.0151 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5994   -1.6346   -0.7598 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6172   -0.6865   -0.1744 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7804    0.3567    0.5328 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3273    1.6941    0.3295 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8264    2.6134   -0.3634 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5265    1.9944    0.9629 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.1698   -0.0223    2.1197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4650    1.6234    1.3503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5068    0.2500    0.8707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9056    0.1927   -1.4140 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2396    0.5733   -1.8940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2566    1.7997   -1.0445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5548   -1.6187   -0.5012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5505   -1.7266    1.0303 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8511   -2.6892   -0.6083 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4745   -1.4549   -1.8541 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1901   -0.2366   -1.0150 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2500   -1.2714    0.5180 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8623    0.1229    1.6306 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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  9  2  0
  8 10  1  0
  7  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  1
M  CHG  2   2   1  10  -1
M  END
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PDB for #<Metabolite:0x00007f46d431b8a8>

HEADER    PROTEIN                                 12-SEP-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-17         0                                  
HETATM    1  C   UNK     0       0.029   3.224   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.060   2.080   0.000  0.00  0.00           N+1
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.795   0.620   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.971   3.157   0.000  0.00  0.00           O-1
HETATM   10  C   UNK     0       2.090   3.224   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    6   10                                             
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    2    7                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    2                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for #<Metabolite:0x00007f46d431b8a8>

COMPND    HMDB0004827
HETATM    1  C1  UNL     1      -1.474   0.523   1.209  1.00  0.00           C  
HETATM    2  N1  UNL     1      -0.571   0.163   0.151  1.00  0.00           N1+
HETATM    3  C2  UNL     1      -0.967   0.733  -1.092  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.646  -1.300   0.015  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.599  -1.635  -0.760  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.617  -0.687  -0.174  1.00  0.00           C  
HETATM    7  C6  UNL     1       0.780   0.357   0.533  1.00  0.00           C  
HETATM    8  C7  UNL     1       1.327   1.694   0.329  1.00  0.00           C  
HETATM    9  O1  UNL     1       0.826   2.613  -0.363  1.00  0.00           O  
HETATM   10  O2  UNL     1       2.526   1.994   0.963  1.00  0.00           O1-
HETATM   11  H1  UNL     1      -1.170  -0.022   2.120  1.00  0.00           H  
HETATM   12  H2  UNL     1      -1.465   1.623   1.350  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.507   0.250   0.871  1.00  0.00           H  
HETATM   14  H4  UNL     1      -1.906   0.193  -1.414  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.240   0.573  -1.894  1.00  0.00           H  
HETATM   16  H6  UNL     1      -1.257   1.800  -1.044  1.00  0.00           H  
HETATM   17  H7  UNL     1      -1.555  -1.619  -0.501  1.00  0.00           H  
HETATM   18  H8  UNL     1      -0.550  -1.727   1.030  1.00  0.00           H  
HETATM   19  H9  UNL     1       0.851  -2.689  -0.608  1.00  0.00           H  
HETATM   20  H10 UNL     1       0.474  -1.455  -1.854  1.00  0.00           H  
HETATM   21  H11 UNL     1       2.190  -0.237  -1.015  1.00  0.00           H  
HETATM   22  H12 UNL     1       2.250  -1.271   0.518  1.00  0.00           H  
HETATM   23  H13 UNL     1       0.862   0.123   1.631  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    4    7
CONECT    3   14   15   16
CONECT    4    5   17   18
CONECT    5    6   19   20
CONECT    6    7   21   22
CONECT    7    8   23
CONECT    8    9    9   10
END
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SMILES for #<Metabolite:0x00007f46d431b8a8>

C[N+]1(C)CCC[C@H]1C([O-])=O
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INCHI for #<Metabolite:0x00007f46d431b8a8>

InChI=1S/C7H13NO2/c1-8(2)5-3-4-6(8)7(9)10/h6H,3-5H2,1-2H3/t6-/m0/s1
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Synonyms
ValueSource
(S)-2-Carboxylato-1,1-dimethylpyrrolidiniumChEBI
N,N-Dimethyl-L-prolineChEBI
StachydrineChEBI
L-Proline betaineKegg
(2S)-2-Carboxy-1,1-dimethylpyrrolidiniumHMDB
(S)-2-Carboxy-1,1-dimethylpyrrolidiniumHMDB
HomostachydrineHMDB
Prestwick-08g03HMDB
DimethylprolineMeSH, HMDB
Stachydrine chlorideMeSH, HMDB
Stachydrine chloride, (S)-isomerMeSH, HMDB
Stachydrine, (+-)-isomerMeSH, HMDB
Proline betaineChEBI
Molecular FormulaC7H13NO2
Average Mass143.1836
Monoisotopic Mass143.094628665
IUPAC Name(2S)-1,1-dimethylpyrrolidin-1-ium-2-carboxylate
Traditional Namestachydrine
CAS Registry NumberNot Available
SMILES
C[N+]1(C)CCC[C@H]1C([O-])=O
InChI Identifier
InChI=1S/C7H13NO2/c1-8(2)5-3-4-6(8)7(9)10/h6H,3-5H2,1-2H3/t6-/m0/s1
InChI KeyCMUNUTVVOOHQPW-LURJTMIESA-N