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Showing metabocard for (2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate (HMDB0242121)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-08-27 00:01:22 UTC
Update Date2021-09-14 15:41:40 UTC
HMDB IDHMDB0242121
Secondary Accession NumbersNone
Metabolite Identification
Common Name(2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate
Description(2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate 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. Based on a literature review very few articles have been published on (2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0242121 ((2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate)

  Mrv1652308272102112D          

 13 13  0  0  1  0            999 V2000
    1.1198    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0157    1.7274    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
    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  1  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  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
    0.5678    1.1143    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.6596   -0.0262    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2287    1.4442    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  6  7  1  6  0  0  0
  8  1  1  0  0  0  0
  8  2  1  0  0  0  0
  8  4  1  0  0  0  0
  8  6  1  0  0  0  0
  5  9  1  6  0  0  0
 10  7  2  0  0  0  0
 11  7  1  0  0  0  0
  5 12  1  1  0  0  0
  6 13  1  1  0  0  0
M  CHG  2   8   1  11  -1
M  END
Download

3D MOL for HMDB0242121 ((2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate)

HMDB0242121
     RDKit          3D
(2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate
 24 24  0  0  0  0  0  0  0  0999 V2000
   -1.9004   -0.1631   -0.8361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6992   -0.0855    0.0085 N   0  0  0  0  0  4  0  0  0  0  0  0
   -1.1265    0.2569    1.3219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1681   -1.4465    0.0517 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3054   -1.3459   -0.1840 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6130    0.0769   -0.5112 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3840    0.6830    0.4970 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2639    0.7482   -0.5894 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3851    2.1038   -0.0761 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1091    2.5521    0.9892 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1212    3.0122   -0.8297 O   0  0  0  0  0  1  0  0  0  0  0  0
   -2.5401    0.7219   -0.7102 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4501   -1.0713   -0.4552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5509   -0.3401   -1.8566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8835    1.0739    1.3500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2873    0.4268    2.0260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6722   -0.6442    1.7329 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3545   -1.9290    1.0389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6054   -2.0997   -0.7086 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9109   -1.6750    0.6963 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6283   -1.9657   -1.0668 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1869    0.2106   -1.4559 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5232    0.0733    1.2586 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0256    0.8263   -1.6912 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
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  8  2  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  3 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  6
  7 23  1  0
  8 24  1  6
M  CHG  2   2   1  11  -1
M  END
Download

3D SDF for HMDB0242121 ((2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate)

  Mrv1652308272102112D          

 13 13  0  0  1  0            999 V2000
    1.1198    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0157    1.7274    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
    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  1  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  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
    0.5678    1.1143    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.6596   -0.0262    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2287    1.4442    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  6  7  1  6  0  0  0
  8  1  1  0  0  0  0
  8  2  1  0  0  0  0
  8  4  1  0  0  0  0
  8  6  1  0  0  0  0
  5  9  1  6  0  0  0
 10  7  2  0  0  0  0
 11  7  1  0  0  0  0
  5 12  1  1  0  0  0
  6 13  1  1  0  0  0
M  CHG  2   8   1  11  -1
M  END
> <DATABASE_ID>
HMDB0242121

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H13NO3/c1-8(2)4-3-5(9)6(8)7(10)11/h5-6,9H,3-4H2,1-2H3/t5-,6+/m0/s1

> <INCHI_KEY>
DJMIFDZBCUUQJN-NTSWFWBYSA-N

> <FORMULA>
C7H13NO3

> <MOLECULAR_WEIGHT>
159.185

> <EXACT_MASS>
159.089543283

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
15.813182088885853

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S)-3-hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate

> <ALOGPS_LOGP>
-1.43

> <JCHEM_LOGP>
-5.024127701138411

> <ALOGPS_LOGS>
-1.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.130689957672523

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.021729377611736

> <JCHEM_PKA_STRONGEST_BASIC>
-3.744738202784416

> <JCHEM_POLAR_SURFACE_AREA>
60.36

> <JCHEM_REFRACTIVITY>
61.4276

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.20e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxystachydrine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0242121 ((2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate)

HMDB0242121
     RDKit          3D
(2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate
 24 24  0  0  0  0  0  0  0  0999 V2000
   -1.9004   -0.1631   -0.8361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6992   -0.0855    0.0085 N   0  0  0  0  0  4  0  0  0  0  0  0
   -1.1265    0.2569    1.3219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1681   -1.4465    0.0517 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3054   -1.3459   -0.1840 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6130    0.0769   -0.5112 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3840    0.6830    0.4970 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2639    0.7482   -0.5894 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3851    2.1038   -0.0761 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1091    2.5521    0.9892 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1212    3.0122   -0.8297 O   0  0  0  0  0  1  0  0  0  0  0  0
   -2.5401    0.7219   -0.7102 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4501   -1.0713   -0.4552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5509   -0.3401   -1.8566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8835    1.0739    1.3500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2873    0.4268    2.0260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6722   -0.6442    1.7329 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3545   -1.9290    1.0389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6054   -2.0997   -0.7086 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9109   -1.6750    0.6963 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6283   -1.9657   -1.0668 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1869    0.2106   -1.4559 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5232    0.0733    1.2586 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0256    0.8263   -1.6912 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
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  8  2  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  3 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  6
  7 23  1  0
  8 24  1  6
M  CHG  2   2   1  11  -1
M  END
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PDB for HMDB0242121 ((2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate)

HEADER    PROTEIN                                 27-AUG-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-AUG-21         0                                  
HETATM    1  C   UNK     0       2.090   3.224   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.029   3.224   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.306   1.175   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  N   UNK     0       1.060   2.080   0.000  0.00  0.00           N+1
HETATM    9  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -1.971   3.157   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -2.795   0.620   0.000  0.00  0.00           O-1
HETATM   12  H   UNK     0      -1.231  -0.049   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0      -0.427   2.696   0.000  0.00  0.00           H+0
CONECT    1    8                                                            
CONECT    2    8                                                            
CONECT    3    4    5                                                       
CONECT    4    3    8                                                       
CONECT    5    3    6    9   12                                             
CONECT    6    5    7    8   13                                             
CONECT    7    6   10   11                                                  
CONECT    8    1    2    4    6                                             
CONECT    9    5                                                            
CONECT   10    7                                                            
CONECT   11    7                                                            
CONECT   12    5                                                            
CONECT   13    6                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END
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3D PDB for HMDB0242121 ((2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate)

COMPND    HMDB0242121
HETATM    1  C1  UNL     1      -1.900  -0.163  -0.836  1.00  0.00           C  
HETATM    2  N1  UNL     1      -0.699  -0.085   0.008  1.00  0.00           N1+
HETATM    3  C2  UNL     1      -1.126   0.257   1.322  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.168  -1.446   0.052  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.305  -1.346  -0.184  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.613   0.077  -0.511  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.384   0.683   0.497  1.00  0.00           O  
HETATM    8  C6  UNL     1       0.264   0.748  -0.589  1.00  0.00           C  
HETATM    9  C7  UNL     1       0.385   2.104  -0.076  1.00  0.00           C  
HETATM   10  O2  UNL     1      -0.109   2.552   0.989  1.00  0.00           O  
HETATM   11  O3  UNL     1       1.121   3.012  -0.830  1.00  0.00           O1-
HETATM   12  H1  UNL     1      -2.540   0.722  -0.710  1.00  0.00           H  
HETATM   13  H2  UNL     1      -2.450  -1.071  -0.455  1.00  0.00           H  
HETATM   14  H3  UNL     1      -1.551  -0.340  -1.857  1.00  0.00           H  
HETATM   15  H4  UNL     1      -1.883   1.074   1.350  1.00  0.00           H  
HETATM   16  H5  UNL     1      -0.287   0.427   2.026  1.00  0.00           H  
HETATM   17  H6  UNL     1      -1.672  -0.644   1.733  1.00  0.00           H  
HETATM   18  H7  UNL     1      -0.355  -1.929   1.039  1.00  0.00           H  
HETATM   19  H8  UNL     1      -0.605  -2.100  -0.709  1.00  0.00           H  
HETATM   20  H9  UNL     1       1.911  -1.675   0.696  1.00  0.00           H  
HETATM   21  H10 UNL     1       1.628  -1.966  -1.067  1.00  0.00           H  
HETATM   22  H11 UNL     1       2.187   0.211  -1.456  1.00  0.00           H  
HETATM   23  H12 UNL     1       2.523   0.073   1.259  1.00  0.00           H  
HETATM   24  H13 UNL     1       0.026   0.826  -1.691  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    4    8
CONECT    3   15   16   17
CONECT    4    5   18   19
CONECT    5    6   20   21
CONECT    6    7    8   22
CONECT    7   23
CONECT    8    9   24
CONECT    9   10   10   11
END
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SMILES for HMDB0242121 ((2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate)

[H][C@]1(O)CC[N+](C)(C)[C@@]1([H])C([O-])=O
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INCHI for HMDB0242121 ((2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate)

InChI=1S/C7H13NO3/c1-8(2)4-3-5(9)6(8)7(10)11/h5-6,9H,3-4H2,1-2H3/t5-,6+/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(2R,3S)-3-Hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylic acidGenerator
Chemical FormulaC7H13NO3
Average Molecular Weight159.185
Monoisotopic Molecular Weight159.089543283
IUPAC Name(2R,3S)-3-hydroxy-1,1-dimethylpyrrolidin-1-ium-2-carboxylate
Traditional Name3-hydroxystachydrine
CAS Registry NumberNot Available
SMILES
[H][C@]1(O)CC[N+](C)(C)[C@@]1([H])C([O-])=O
InChI Identifier
InChI=1S/C7H13NO3/c1-8(2)4-3-5(9)6(8)7(10)11/h5-6,9H,3-4H2,1-2H3/t5-,6+/m0/s1
InChI KeyDJMIFDZBCUUQJN-NTSWFWBYSA-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
  • D-alpha-amino acid
  • Pyrrolidine carboxylic acid
  • Pyrrolidine carboxylic acid or derivatives
  • Beta-hydroxy acid
  • Hydroxy acid
  • N-alkylpyrrolidine
  • Tetraalkylammonium salt
  • Pyrrolidine
  • Quaternary ammonium salt
  • Secondary alcohol
  • Carboxylic acid salt
  • Azacycle
  • Organoheterocyclic compound
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Alcohol
  • Carbonyl group
  • Organic oxygen compound
  • Amine
  • Organic salt
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
DispositionNot Available
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 LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID391002
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound442640
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Kong SW, Hernandez-Ferrer C: Assessment of coverage for endogenous metabolites and exogenous chemical compounds using an untargeted metabolomics platform. Pac Symp Biocomput. 2020;25:587-598. [PubMed:31797630 ]