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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-23 02:58:21 UTC

Update Date

2021-09-23 02:58:21 UTC

HMDB ID

HMDB0301842

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Cucumopine

Description

Cucumopine, also known as mikimopine or cucumopine, (4r-cis)-isomer, is a member of the class of compounds known as L-alpha-amino acids. L-alpha-amino acids are alpha amino acids which have the L-configuration of the alpha-carbon atom. Cucumopine is slightly soluble (in water) and a moderately acidic compound (based on its pKa). Cucumopine can be found in carrot and wild carrot, which makes cucumopine a potential biomarker for the consumption of these food products.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0301842
     RDKit          3D
Cucumopine
 33 34  0  0  0  0  0  0  0  0999 V2000
    3.3984   -2.2679    0.0551 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2509   -1.0395    0.1723 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0449   -0.2299   -0.6626 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3088   -0.4017    1.1178 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3402    0.5003    0.5356 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3345    0.1134   -0.4737 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7702   -0.3974   -1.7627 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4857    0.2866   -2.8177 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4610   -1.5283   -2.0841 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4362    1.3277   -0.7203 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8238    1.2733   -0.5671 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3138    2.6980   -0.4731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5412    3.6800   -0.5416 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6803    2.8699   -0.3047 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1679    0.6973    0.8183 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7370   -0.6988    0.7463 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2671   -1.8498    1.1645 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4277   -2.8743    0.8169 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3806   -2.3015    0.1784 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5462   -0.9701    0.1229 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6758    0.4696   -0.2661 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9230   -1.1283    1.8721 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0032    0.2273    1.7739 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9274    1.4180    0.1850 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7420    0.9675    1.3901 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0891   -2.3810   -2.4761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0202    2.1796   -0.3438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4041    0.7256   -1.3360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9701    3.3526    0.5604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6239    1.2474    1.5900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2669    0.8165    0.9220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5643   -3.9266    1.0075 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4162   -2.8553   -0.1996 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  6
  7  8  2  0
  7  9  1  0
  6 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 11 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 20  6  1  0
 20 16  2  0
  3 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  9 26  1  0
 10 27  1  0
 11 28  1  6
 14 29  1  0
 15 30  1  0
 15 31  1  0
 18 32  1  0
 19 33  1  0
M  END


  Mrv0541 02241221452D          

 21 22  0  0  1  0            999 V2000
    6.3037   -6.3843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5892   -5.9717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8747   -6.3842    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5893   -5.1468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8748   -4.7343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8748   -3.9092    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1604   -3.4968    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3757   -3.7517    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8908   -3.0843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3758   -2.4168    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1604   -2.6718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8748   -2.2593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5893   -2.6718    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.3038   -2.2593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0182   -2.6718    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3038   -1.4343    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5893   -3.4968    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5893   -1.8468    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1603   -4.3217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3634   -4.5352    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4760   -5.0839    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
  7 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 13 17  1  0  0  0  0
  6 17  1  0  0  0  0
 13 18  1  6  0  0  0
  6 19  1  6  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0301842

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@]1(CC2=C(NC=N2)[C@](CCC(O)=O)(N1)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H13N3O6/c15-7(16)1-2-11(10(19)20)8-5(12-4-13-8)3-6(14-11)9(17)18/h4,6,14H,1-3H2,(H,12,13)(H,15,16)(H,17,18)(H,19,20)/t6-,11-/m0/s1

> <INCHI_KEY>
XGCZNSAJOHDWQS-KGFZYKRKSA-N

> <FORMULA>
C11H13N3O6

> <MOLECULAR_WEIGHT>
283.2374

> <EXACT_MASS>
283.080435163

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
25.338530578767337

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S,6S)-4-(2-carboxyethyl)-3H,4H,5H,6H,7H-imidazo[4,5-c]pyridine-4,6-dicarboxylic acid

> <ALOGPS_LOGP>
-1.09

> <JCHEM_LOGP>
-4.528557826204238

> <ALOGPS_LOGS>
-1.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.65037174543189

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.9590349709861057

> <JCHEM_PKA_STRONGEST_BASIC>
7.013942437811194

> <JCHEM_POLAR_SURFACE_AREA>
152.60999999999999

> <JCHEM_REFRACTIVITY>
62.03360000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.89e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cucumopine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0301842
     RDKit          3D
Cucumopine
 33 34  0  0  0  0  0  0  0  0999 V2000
    3.3984   -2.2679    0.0551 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2509   -1.0395    0.1723 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0449   -0.2299   -0.6626 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3088   -0.4017    1.1178 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3402    0.5003    0.5356 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3345    0.1134   -0.4737 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7702   -0.3974   -1.7627 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4857    0.2866   -2.8177 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4610   -1.5283   -2.0841 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4362    1.3277   -0.7203 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8238    1.2733   -0.5671 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3138    2.6980   -0.4731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5412    3.6800   -0.5416 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6803    2.8699   -0.3047 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1679    0.6973    0.8183 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7370   -0.6988    0.7463 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2671   -1.8498    1.1645 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4277   -2.8743    0.8169 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3806   -2.3015    0.1784 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5462   -0.9701    0.1229 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6758    0.4696   -0.2661 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9230   -1.1283    1.8721 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0032    0.2273    1.7739 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9274    1.4180    0.1850 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7420    0.9675    1.3901 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0891   -2.3810   -2.4761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0202    2.1796   -0.3438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4041    0.7256   -1.3360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9701    3.3526    0.5604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6239    1.2474    1.5900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2669    0.8165    0.9220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5643   -3.9266    1.0075 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4162   -2.8553   -0.1996 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  6
  7  8  2  0
  7  9  1  0
  6 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 11 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 20  6  1  0
 20 16  2  0
  3 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  9 26  1  0
 10 27  1  0
 11 28  1  6
 14 29  1  0
 15 30  1  0
 15 31  1  0
 18 32  1  0
 19 33  1  0
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0      11.767 -11.917   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      10.433 -11.147   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       9.099 -11.917   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      10.433  -9.607   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.100  -8.837   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.100  -7.297   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.766  -6.527   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       6.301  -7.003   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       5.396  -5.757   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       6.301  -4.511   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       7.766  -4.987   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.100  -4.217   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.433  -4.987   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.767  -4.217   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      13.101  -4.987   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      11.767  -2.677   0.000  0.00  0.00           O+0
HETATM   17  N   UNK     0      10.433  -6.527   0.000  0.00  0.00           N+0
HETATM   18  H   UNK     0      10.433  -3.447   0.000  0.00  0.00           H+0
HETATM   19  C   UNK     0       7.766  -8.067   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       6.278  -8.466   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       8.355  -9.490   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   17   19                                             
CONECT    7    6    8   11                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    7   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   17   18                                             
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   13    6                                                       
CONECT   18   13                                                            
CONECT   19    6   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

COMPND    HMDB0301842
HETATM    1  O1  UNL     1       3.398  -2.268   0.055  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.251  -1.040   0.172  1.00  0.00           C  
HETATM    3  O2  UNL     1       4.045  -0.230  -0.663  1.00  0.00           O  
HETATM    4  C2  UNL     1       2.309  -0.402   1.118  1.00  0.00           C  
HETATM    5  C3  UNL     1       1.340   0.500   0.536  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.334   0.113  -0.474  1.00  0.00           C  
HETATM    7  C5  UNL     1       0.770  -0.397  -1.763  1.00  0.00           C  
HETATM    8  O3  UNL     1       0.486   0.287  -2.818  1.00  0.00           O  
HETATM    9  O4  UNL     1       1.461  -1.528  -2.084  1.00  0.00           O  
HETATM   10  N1  UNL     1      -0.436   1.328  -0.720  1.00  0.00           N  
HETATM   11  C6  UNL     1      -1.824   1.273  -0.567  1.00  0.00           C  
HETATM   12  C7  UNL     1      -2.314   2.698  -0.473  1.00  0.00           C  
HETATM   13  O5  UNL     1      -1.541   3.680  -0.542  1.00  0.00           O  
HETATM   14  O6  UNL     1      -3.680   2.870  -0.305  1.00  0.00           O  
HETATM   15  C8  UNL     1      -2.168   0.697   0.818  1.00  0.00           C  
HETATM   16  C9  UNL     1      -1.737  -0.699   0.746  1.00  0.00           C  
HETATM   17  N2  UNL     1      -2.267  -1.850   1.165  1.00  0.00           N  
HETATM   18  C10 UNL     1      -1.428  -2.874   0.817  1.00  0.00           C  
HETATM   19  N3  UNL     1      -0.381  -2.301   0.178  1.00  0.00           N  
HETATM   20  C11 UNL     1      -0.546  -0.970   0.123  1.00  0.00           C  
HETATM   21  H1  UNL     1       4.676   0.470  -0.266  1.00  0.00           H  
HETATM   22  H2  UNL     1       1.923  -1.128   1.872  1.00  0.00           H  
HETATM   23  H3  UNL     1       3.003   0.227   1.774  1.00  0.00           H  
HETATM   24  H4  UNL     1       1.927   1.418   0.185  1.00  0.00           H  
HETATM   25  H5  UNL     1       0.742   0.968   1.390  1.00  0.00           H  
HETATM   26  H6  UNL     1       1.089  -2.381  -2.476  1.00  0.00           H  
HETATM   27  H7  UNL     1      -0.020   2.180  -0.344  1.00  0.00           H  
HETATM   28  H8  UNL     1      -2.404   0.726  -1.336  1.00  0.00           H  
HETATM   29  H9  UNL     1      -3.970   3.353   0.560  1.00  0.00           H  
HETATM   30  H10 UNL     1      -1.624   1.247   1.590  1.00  0.00           H  
HETATM   31  H11 UNL     1      -3.267   0.816   0.922  1.00  0.00           H  
HETATM   32  H12 UNL     1      -1.564  -3.927   1.007  1.00  0.00           H  
HETATM   33  H13 UNL     1       0.416  -2.855  -0.200  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   21
CONECT    4    5   22   23
CONECT    5    6   24   25
CONECT    6    7   10   20
CONECT    7    8    8    9
CONECT    9   26
CONECT   10   11   27
CONECT   11   12   15   28
CONECT   12   13   13   14
CONECT   14   29
CONECT   15   16   30   31
CONECT   16   17   20   20
CONECT   17   18   18
CONECT   18   19   32
CONECT   19   20   33
END

HMDB0301842
     RDKit          3D
Cucumopine
 33 34  0  0  0  0  0  0  0  0999 V2000
    3.3984   -2.2679    0.0551 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2509   -1.0395    0.1723 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0449   -0.2299   -0.6626 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3088   -0.4017    1.1178 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3402    0.5003    0.5356 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3345    0.1134   -0.4737 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7702   -0.3974   -1.7627 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4857    0.2866   -2.8177 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4610   -1.5283   -2.0841 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4362    1.3277   -0.7203 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8238    1.2733   -0.5671 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3138    2.6980   -0.4731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5412    3.6800   -0.5416 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6803    2.8699   -0.3047 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1679    0.6973    0.8183 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7370   -0.6988    0.7463 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2671   -1.8498    1.1645 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4277   -2.8743    0.8169 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3806   -2.3015    0.1784 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5462   -0.9701    0.1229 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6758    0.4696   -0.2661 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9230   -1.1283    1.8721 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0032    0.2273    1.7739 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9274    1.4180    0.1850 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7420    0.9675    1.3901 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0891   -2.3810   -2.4761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0202    2.1796   -0.3438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4041    0.7256   -1.3360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9701    3.3526    0.5604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6239    1.2474    1.5900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2669    0.8165    0.9220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5643   -3.9266    1.0075 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4162   -2.8553   -0.1996 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  6
  7  8  2  0
  7  9  1  0
  6 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 11 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 20  6  1  0
 20 16  2  0
  3 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  9 26  1  0
 10 27  1  0
 11 28  1  6
 14 29  1  0
 15 30  1  0
 15 31  1  0
 18 32  1  0
 19 33  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(4S,6S)-4-(2-Carboxyethyl)-3H,4H,5H,6H,7H-imidazo[4,5-c]pyridine-4,6-dicarboxylate	Generator

Chemical Formula

C₁₁H₁₃N₃O₆

Average Molecular Weight

283.2374

Monoisotopic Molecular Weight

283.080435163

IUPAC Name

(4S,6S)-4-(2-carboxyethyl)-3H,4H,5H,6H,7H-imidazo[4,5-c]pyridine-4,6-dicarboxylic acid

Traditional Name

cucumopine

CAS Registry Number

Not Available

SMILES

[H][C@]1(CC2=C(NC=N2)[C@](CCC(O)=O)(N1)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C11H13N3O6/c15-7(16)1-2-11(10(19)20)8-5(12-4-13-8)3-6(14-11)9(17)18/h4,6,14H,1-3H2,(H,12,13)(H,15,16)(H,17,18)(H,19,20)/t6-,11-/m0/s1

InChI Key

XGCZNSAJOHDWQS-KGFZYKRKSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Substituents

L-alpha-amino acid
Imidazopiperidine
Imidazopyridine
Tricarboxylic acid or derivatives
Aralkylamine
Azole
Imidazole
Heteroaromatic compound
Amino acid
Azacycle
Organoheterocyclic compound
Secondary amine
Secondary aliphatic amine
Carboxylic acid
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Amine
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

non-proteinogenic alpha-amino acid (CHEBI:3937 )

Ontology

Not Available

Carrot (FooDB: FOOD00245)
Wild carrot (FooDB: FOOD00072)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-1.1	ALOGPS
logP	-4.5	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.96	ChemAxon
pKa (Strongest Basic)	7.01	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	152.61 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	62.03 m³·mol⁻¹	ChemAxon
Polarizability	25.34 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
AllCCS	[M+H]+	162.371	32859911
AllCCS	[M+H-H2O]+	158.912	32859911
AllCCS	[M+Na]+	166.501	32859911
AllCCS	[M+NH4]+	165.579	32859911
AllCCS	[M-H]-	160.991	32859911
AllCCS	[M+Na-2H]-	160.743	32859911
AllCCS	[M+HCOO]-	160.589	32859911
DeepCCS	[M+H]+	156.621	30932474
DeepCCS	[M-H]-	154.263	30932474
DeepCCS	[M-2H]-	188.221	30932474
DeepCCS	[M+Na]+	163.833	30932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Cucumopine,4TMS,isomer #1	C[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C)C2=C(C[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C)N=C[NH]2	2587.7	Semi standard non polar	33892256
Cucumopine,4TMS,isomer #1	C[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C)C2=C(C[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C)N=C[NH]2	2623.1	Standard non polar	33892256
Cucumopine,4TMS,isomer #1	C[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C)C2=C(C[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C)N=C[NH]2	3148.5	Standard polar	33892256
Cucumopine,4TMS,isomer #2	C[Si](C)(C)OC(=O)CC[C@]1(C(=O)O[Si](C)(C)C)N[C@H](C(=O)O[Si](C)(C)C)CC2=C1N([Si](C)(C)C)C=N2	2694.4	Semi standard non polar	33892256
Cucumopine,4TMS,isomer #2	C[Si](C)(C)OC(=O)CC[C@]1(C(=O)O[Si](C)(C)C)N[C@H](C(=O)O[Si](C)(C)C)CC2=C1N([Si](C)(C)C)C=N2	2560.7	Standard non polar	33892256
Cucumopine,4TMS,isomer #2	C[Si](C)(C)OC(=O)CC[C@]1(C(=O)O[Si](C)(C)C)N[C@H](C(=O)O[Si](C)(C)C)CC2=C1N([Si](C)(C)C)C=N2	3346.4	Standard polar	33892256
Cucumopine,4TMS,isomer #3	C[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C)C2=C(C[C@@H](C(=O)O)N1[Si](C)(C)C)N=CN2[Si](C)(C)C	2655.7	Semi standard non polar	33892256
Cucumopine,4TMS,isomer #3	C[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C)C2=C(C[C@@H](C(=O)O)N1[Si](C)(C)C)N=CN2[Si](C)(C)C	2669.5	Standard non polar	33892256
Cucumopine,4TMS,isomer #3	C[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C)C2=C(C[C@@H](C(=O)O)N1[Si](C)(C)C)N=CN2[Si](C)(C)C	3288.2	Standard polar	33892256
Cucumopine,4TMS,isomer #4	C[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O)C2=C(C[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C)N=CN2[Si](C)(C)C	2675.9	Semi standard non polar	33892256
Cucumopine,4TMS,isomer #4	C[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O)C2=C(C[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C)N=CN2[Si](C)(C)C	2652.3	Standard non polar	33892256
Cucumopine,4TMS,isomer #4	C[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O)C2=C(C[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C)N=CN2[Si](C)(C)C	3259.6	Standard polar	33892256
Cucumopine,4TMS,isomer #5	C[Si](C)(C)OC(=O)[C@@H]1CC2=C(N([Si](C)(C)C)C=N2)[C@@](CCC(=O)O)(C(=O)O[Si](C)(C)C)N1[Si](C)(C)C	2675.5	Semi standard non polar	33892256
Cucumopine,4TMS,isomer #5	C[Si](C)(C)OC(=O)[C@@H]1CC2=C(N([Si](C)(C)C)C=N2)[C@@](CCC(=O)O)(C(=O)O[Si](C)(C)C)N1[Si](C)(C)C	2662.4	Standard non polar	33892256
Cucumopine,4TMS,isomer #5	C[Si](C)(C)OC(=O)[C@@H]1CC2=C(N([Si](C)(C)C)C=N2)[C@@](CCC(=O)O)(C(=O)O[Si](C)(C)C)N1[Si](C)(C)C	3212.0	Standard polar	33892256
Cucumopine,5TMS,isomer #1	C[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C)C2=C(C[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C)N=CN2[Si](C)(C)C	2700.4	Semi standard non polar	33892256
Cucumopine,5TMS,isomer #1	C[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C)C2=C(C[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C)N=CN2[Si](C)(C)C	2692.7	Standard non polar	33892256
Cucumopine,5TMS,isomer #1	C[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C)C2=C(C[C@@H](C(=O)O[Si](C)(C)C)N1[Si](C)(C)C)N=CN2[Si](C)(C)C	3041.0	Standard polar	33892256
Cucumopine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C(C)(C)C)C2=C(C[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C)N=C[NH]2	3444.3	Semi standard non polar	33892256
Cucumopine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C(C)(C)C)C2=C(C[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C)N=C[NH]2	3451.6	Standard non polar	33892256
Cucumopine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C(C)(C)C)C2=C(C[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C)N=C[NH]2	3434.7	Standard polar	33892256
Cucumopine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CC[C@]1(C(=O)O[Si](C)(C)C(C)(C)C)N[C@H](C(=O)O[Si](C)(C)C(C)(C)C)CC2=C1N([Si](C)(C)C(C)(C)C)C=N2	3506.8	Semi standard non polar	33892256
Cucumopine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CC[C@]1(C(=O)O[Si](C)(C)C(C)(C)C)N[C@H](C(=O)O[Si](C)(C)C(C)(C)C)CC2=C1N([Si](C)(C)C(C)(C)C)C=N2	3310.7	Standard non polar	33892256
Cucumopine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CC[C@]1(C(=O)O[Si](C)(C)C(C)(C)C)N[C@H](C(=O)O[Si](C)(C)C(C)(C)C)CC2=C1N([Si](C)(C)C(C)(C)C)C=N2	3567.1	Standard polar	33892256
Cucumopine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C(C)(C)C)C2=C(C[C@@H](C(=O)O)N1[Si](C)(C)C(C)(C)C)N=CN2[Si](C)(C)C(C)(C)C	3532.8	Semi standard non polar	33892256
Cucumopine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C(C)(C)C)C2=C(C[C@@H](C(=O)O)N1[Si](C)(C)C(C)(C)C)N=CN2[Si](C)(C)C(C)(C)C	3448.1	Standard non polar	33892256
Cucumopine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C(C)(C)C)C2=C(C[C@@H](C(=O)O)N1[Si](C)(C)C(C)(C)C)N=CN2[Si](C)(C)C(C)(C)C	3514.1	Standard polar	33892256
Cucumopine,4TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O)C2=C(C[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C)N=CN2[Si](C)(C)C(C)(C)C	3553.9	Semi standard non polar	33892256
Cucumopine,4TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O)C2=C(C[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C)N=CN2[Si](C)(C)C(C)(C)C	3413.8	Standard non polar	33892256
Cucumopine,4TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O)C2=C(C[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C)N=CN2[Si](C)(C)C(C)(C)C	3503.4	Standard polar	33892256
Cucumopine,4TBDMS,isomer #5	CC(C)(C)[Si](C)(C)OC(=O)[C@@H]1CC2=C(N([Si](C)(C)C(C)(C)C)C=N2)[C@@](CCC(=O)O)(C(=O)O[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	3539.5	Semi standard non polar	33892256
Cucumopine,4TBDMS,isomer #5	CC(C)(C)[Si](C)(C)OC(=O)[C@@H]1CC2=C(N([Si](C)(C)C(C)(C)C)C=N2)[C@@](CCC(=O)O)(C(=O)O[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	3419.6	Standard non polar	33892256
Cucumopine,4TBDMS,isomer #5	CC(C)(C)[Si](C)(C)OC(=O)[C@@H]1CC2=C(N([Si](C)(C)C(C)(C)C)C=N2)[C@@](CCC(=O)O)(C(=O)O[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	3469.8	Standard polar	33892256
Cucumopine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C(C)(C)C)C2=C(C[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C)N=CN2[Si](C)(C)C(C)(C)C	3665.5	Semi standard non polar	33892256
Cucumopine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C(C)(C)C)C2=C(C[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C)N=CN2[Si](C)(C)C(C)(C)C	3593.7	Standard non polar	33892256
Cucumopine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CC[C@@]1(C(=O)O[Si](C)(C)C(C)(C)C)C2=C(C[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C)N=CN2[Si](C)(C)C(C)(C)C	3399.4	Standard polar	33892256

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucumopine 10V, Positive-QTOF	splash10-00s9-0090000000-fc422d29d3dd64b9fa6e	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucumopine 20V, Positive-QTOF	splash10-007c-1690000000-70320eb29cfcf777b400	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucumopine 40V, Positive-QTOF	splash10-0006-1910000000-07a69b0849f5b1d0c2cf	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucumopine 10V, Negative-QTOF	splash10-0019-0290000000-170ec985d2aa7ac4e1fb	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucumopine 20V, Negative-QTOF	splash10-000l-0690000000-986270ce11025bd4ac72	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucumopine 40V, Negative-QTOF	splash10-0006-5920000000-3e2bede5b37bb625cbc8	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucumopine 10V, Positive-QTOF	splash10-001i-0090000000-6df49d2a9f857a0abbb1	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucumopine 20V, Positive-QTOF	splash10-00ec-1490000000-30752b2537f33d5cce63	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucumopine 40V, Positive-QTOF	splash10-00kf-2910000000-ab4e965e5e5192b37e86	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucumopine 10V, Negative-QTOF	splash10-0006-0940000000-9a65682a30ac18db6bb5	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucumopine 20V, Negative-QTOF	splash10-0006-0960000000-b62608f08f59e8314f08	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucumopine 40V, Negative-QTOF	splash10-0006-2910000000-93781a6d2e0225a35038	2021-10-21	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1814131

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for Cucumopine (HMDB0301842)

MOL for HMDB0301842 (Cucumopine)

3D MOL for HMDB0301842 (Cucumopine)

3D SDF for HMDB0301842 (Cucumopine)

3D-SDF for HMDB0301842 (Cucumopine)

PDB for HMDB0301842 (Cucumopine)

3D PDB for HMDB0301842 (Cucumopine)

SMILES for HMDB0301842 (Cucumopine)

INCHI for HMDB0301842 (Cucumopine)

Structure for HMDB0301842 (Cucumopine)

3D Structure for HMDB0301842 (Cucumopine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

MS/MS Spectra