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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 19:21:52 UTC

Update Date

2021-09-26 23:14:51 UTC

HMDB ID

HMDB0258148

Secondary Accession Numbers

None

Metabolite Identification

Common Name

N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide

Description

N-[5-hydroxy-3-(prop-2-en-1-yldisulfanyl)pent-2-en-2-yl]-N-[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl]formamide belongs to the class of organic compounds known as aminopyrimidines and derivatives. These are organic compounds containing an amino group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Based on a literature review very few articles have been published on N-[5-hydroxy-3-(prop-2-en-1-yldisulfanyl)pent-2-en-2-yl]-N-[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl]formamide. This compound has been identified in human blood as reported by (PMID: 31557052 ). N-[(4-amino-2-methylpyrimidin-5-yl)methyl]-n-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide 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

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

HMDB0258148
     RDKit          3D
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfa...
 45 45  0  0  0  0  0  0  0  0999 V2000
    4.8132    3.7234   -0.3895 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5172    3.1155    0.7160 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5557    1.9865    0.7632 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9573    1.6511   -0.8760 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.1114   -0.3490   -1.3457 S   0  0  0  0  0  0  0  0  0  0  0  0
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    2.7702   -3.4897    0.5652 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6161   -1.0554   -0.3741 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1533004161522482D          

 23 23  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
HMDB0258148

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(N(CC1=CN=C(C)N=C1N)C=O)=C(CCO)SSCC=C

> <INCHI_IDENTIFIER>
InChI=1S/C15H22N4O2S2/c1-4-7-22-23-14(5-6-20)11(2)19(10-21)9-13-8-17-12(3)18-15(13)16/h4,8,10,20H,1,5-7,9H2,2-3H3,(H2,16,17,18)

> <INCHI_KEY>
WNCAVNGLACHSRZ-UHFFFAOYSA-N

> <FORMULA>
C15H22N4O2S2

> <MOLECULAR_WEIGHT>
354.49

> <EXACT_MASS>
354.118418312

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
45

> <JCHEM_AVERAGE_POLARIZABILITY>
37.17545685696899

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
N-[(4-amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-en-1-yldisulfanyl)pent-2-en-2-yl]formamide

> <ALOGPS_LOGP>
1.59

> <JCHEM_LOGP>
0.14866769299999988

> <ALOGPS_LOGS>
-3.49

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.898106717068003

> <JCHEM_PKA_STRONGEST_BASIC>
6.259375270271024

> <JCHEM_POLAR_SURFACE_AREA>
92.34

> <JCHEM_REFRACTIVITY>
102.3386

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.15e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(4-amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-en-1-yldisulfanyl)pent-2-en-2-yl]formamide

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0258148
     RDKit          3D
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfa...
 45 45  0  0  0  0  0  0  0  0999 V2000
    4.8132    3.7234   -0.3895 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5172    3.1155    0.7160 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5557    1.9865    0.7632 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9573    1.6511   -0.8760 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.1114   -0.3490   -1.3457 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.6825   -1.3810   -1.0408 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8894   -2.8067   -1.5007 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7791   -3.7961   -0.3943 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.6161   -1.0554   -0.3741 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.1418   -2.7134   -1.0016 C   0  0  0  0  0  0  0  0  0  0  0  0
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 23 45  1  0
M  END

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.334 -11.550   0.000  0.00  0.00           O+0
HETATM    7  S   UNK     0      -1.334  -6.930   0.000  0.00  0.00           S+0
HETATM    8  S   UNK     0       0.000  -7.700   0.000  0.00  0.00           S+0
HETATM    9  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -5.335  -7.700   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      -5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      -8.002 -12.320   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      -9.336 -11.550   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0     -10.669 -12.320   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      -9.336 -10.010   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      -8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      -8.002  -7.700   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      -6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -6.668  -5.390   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    3    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    2   13   22                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   20                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   14   21                                                  
CONECT   21   20                                                            
CONECT   22   12   23                                                       
CONECT   23   22                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

COMPND    HMDB0258148
HETATM    1  C1  UNL     1       4.813   3.723  -0.390  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.517   3.116   0.716  1.00  0.00           C  
HETATM    3  C3  UNL     1       3.556   1.987   0.763  1.00  0.00           C  
HETATM    4  S1  UNL     1       2.957   1.651  -0.876  1.00  0.00           S  
HETATM    5  S2  UNL     1       3.111  -0.349  -1.346  1.00  0.00           S  
HETATM    6  C4  UNL     1       1.683  -1.381  -1.041  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.889  -2.807  -1.501  1.00  0.00           C  
HETATM    8  C6  UNL     1       1.779  -3.796  -0.394  1.00  0.00           C  
HETATM    9  O1  UNL     1       2.770  -3.490   0.565  1.00  0.00           O  
HETATM   10  C7  UNL     1       0.616  -1.055  -0.374  1.00  0.00           C  
HETATM   11  C8  UNL     1       0.667   0.373   0.205  1.00  0.00           C  
HETATM   12  N1  UNL     1      -0.626  -1.650  -0.242  1.00  0.00           N  
HETATM   13  C9  UNL     1      -1.142  -2.713  -1.002  1.00  0.00           C  
HETATM   14  O2  UNL     1      -2.328  -3.179  -0.752  1.00  0.00           O  
HETATM   15  C10 UNL     1      -1.550  -1.189   0.823  1.00  0.00           C  
HETATM   16  C11 UNL     1      -2.445  -0.104   0.357  1.00  0.00           C  
HETATM   17  C12 UNL     1      -2.414   0.424  -0.909  1.00  0.00           C  
HETATM   18  N2  UNL     1      -3.233   1.432  -1.253  1.00  0.00           N  
HETATM   19  C13 UNL     1      -4.097   1.950  -0.381  1.00  0.00           C  
HETATM   20  C14 UNL     1      -4.974   3.071  -0.770  1.00  0.00           C  
HETATM   21  N3  UNL     1      -4.127   1.429   0.865  1.00  0.00           N  
HETATM   22  C15 UNL     1      -3.349   0.427   1.285  1.00  0.00           C  
HETATM   23  N4  UNL     1      -3.468  -0.028   2.616  1.00  0.00           N  
HETATM   24  H1  UNL     1       4.368   3.427  -1.356  1.00  0.00           H  
HETATM   25  H2  UNL     1       5.501   4.544  -0.413  1.00  0.00           H  
HETATM   26  H3  UNL     1       5.007   3.461   1.643  1.00  0.00           H  
HETATM   27  H4  UNL     1       2.722   2.297   1.457  1.00  0.00           H  
HETATM   28  H5  UNL     1       4.127   1.135   1.209  1.00  0.00           H  
HETATM   29  H6  UNL     1       2.999  -2.929  -1.840  1.00  0.00           H  
HETATM   30  H7  UNL     1       1.357  -2.945  -2.414  1.00  0.00           H  
HETATM   31  H8  UNL     1       0.860  -3.950   0.123  1.00  0.00           H  
HETATM   32  H9  UNL     1       2.059  -4.802  -0.841  1.00  0.00           H  
HETATM   33  H10 UNL     1       2.428  -3.723   1.461  1.00  0.00           H  
HETATM   34  H11 UNL     1       1.480   0.309   0.918  1.00  0.00           H  
HETATM   35  H12 UNL     1       0.718   1.014  -0.659  1.00  0.00           H  
HETATM   36  H13 UNL     1      -0.227   0.635   0.770  1.00  0.00           H  
HETATM   37  H14 UNL     1      -0.683  -3.242  -1.813  1.00  0.00           H  
HETATM   38  H15 UNL     1      -2.149  -2.070   1.184  1.00  0.00           H  
HETATM   39  H16 UNL     1      -0.993  -0.853   1.698  1.00  0.00           H  
HETATM   40  H17 UNL     1      -1.713   0.021  -1.649  1.00  0.00           H  
HETATM   41  H18 UNL     1      -4.553   3.528  -1.706  1.00  0.00           H  
HETATM   42  H19 UNL     1      -6.009   2.805  -0.953  1.00  0.00           H  
HETATM   43  H20 UNL     1      -4.890   3.877   0.002  1.00  0.00           H  
HETATM   44  H21 UNL     1      -3.628  -1.025   2.819  1.00  0.00           H  
HETATM   45  H22 UNL     1      -3.388   0.646   3.394  1.00  0.00           H  
CONECT    1    2    2   24   25
CONECT    2    3   26
CONECT    3    4   27   28
CONECT    4    5
CONECT    5    6
CONECT    6    7   10   10
CONECT    7    8   29   30
CONECT    8    9   31   32
CONECT    9   33
CONECT   10   11   12
CONECT   11   34   35   36
CONECT   12   13   15
CONECT   13   14   14   37
CONECT   15   16   38   39
CONECT   16   17   17   22
CONECT   17   18   40
CONECT   18   19   19
CONECT   19   20   21
CONECT   20   41   42   43
CONECT   21   22   22
CONECT   22   23
CONECT   23   44   45
END

HMDB0258148
     RDKit          3D
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfa...
 45 45  0  0  0  0  0  0  0  0999 V2000
    4.8132    3.7234   -0.3895 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5172    3.1155    0.7160 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5557    1.9865    0.7632 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9573    1.6511   -0.8760 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.1114   -0.3490   -1.3457 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.6825   -1.3810   -1.0408 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8894   -2.8067   -1.5007 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7791   -3.7961   -0.3943 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7702   -3.4897    0.5652 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6161   -1.0554   -0.3741 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6671    0.3727    0.2052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6258   -1.6499   -0.2421 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1418   -2.7134   -1.0016 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3282   -3.1791   -0.7520 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5495   -1.1886    0.8232 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4448   -0.1041    0.3565 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4144    0.4238   -0.9086 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2327    1.4318   -1.2533 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0969    1.9505   -0.3808 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9736    3.0706   -0.7697 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1272    1.4288    0.8651 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3485    0.4274    1.2846 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4683   -0.0279    2.6156 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3683    3.4266   -1.3560 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5013    4.5443   -0.4126 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0068    3.4606    1.6431 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7222    2.2972    1.4565 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1265    1.1349    1.2089 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9991   -2.9290   -1.8397 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3566   -2.9449   -2.4143 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8603   -3.9505    0.1231 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0588   -4.8020   -0.8405 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4281   -3.7225    1.4607 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4802    0.3094    0.9182 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7180    1.0136   -0.6589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2266    0.6347    0.7700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6833   -3.2425   -1.8128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1490   -2.0698    1.1844 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9933   -0.8532    1.6983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7130    0.0210   -1.6488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5533    3.5278   -1.7058 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0090    2.8052   -0.9530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8900    3.8769    0.0015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6285   -1.0254    2.8186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3877    0.6463    3.3937 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  6 10  2  3
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  2  0
 12 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 19 21  1  0
 21 22  2  0
 22 23  1  0
 22 16  1  0
  1 24  1  0
  1 25  1  0
  2 26  1  0
  3 27  1  0
  3 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  8 32  1  0
  9 33  1  0
 11 34  1  0
 11 35  1  0
 11 36  1  0
 13 37  1  0
 15 38  1  0
 15 39  1  0
 17 40  1  0
 20 41  1  0
 20 42  1  0
 20 43  1  0
 23 44  1  0
 23 45  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
N-[5-Hydroxy-3-(prop-2-en-1-yldisulphanyl)pent-2-en-2-yl]-N-[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl]formamide	Generator
Allithiamine hydrochloride	MeSH

Chemical Formula

C₁₅H₂₂N₄O₂S₂

Average Molecular Weight

354.49

Monoisotopic Molecular Weight

354.118418312

IUPAC Name

N-[(4-amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-en-1-yldisulfanyl)pent-2-en-2-yl]formamide

Traditional Name

N-[(4-amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-en-1-yldisulfanyl)pent-2-en-2-yl]formamide

CAS Registry Number

Not Available

SMILES

CC(N(CC1=CN=C(C)N=C1N)C=O)=C(CCO)SSCC=C

InChI Identifier

InChI=1S/C15H22N4O2S2/c1-4-7-22-23-14(5-6-20)11(2)19(10-21)9-13-8-17-12(3)18-15(13)16/h4,8,10,20H,1,5-7,9H2,2-3H3,(H2,16,17,18)

InChI Key

WNCAVNGLACHSRZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminopyrimidines and derivatives. These are organic compounds containing an amino group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Aminopyrimidines and derivatives

Alternative Parents

Substituents

Aminopyrimidine
Primary aromatic amine
Imidolactam
Tertiary carboxylic acid amide
Heteroaromatic compound
Amino acid or derivatives
Carboxamide group
Organic disulfide
Allyl sulfur compound
Sulfenyl compound
Azacycle
Carboxylic acid derivative
Hydrocarbon derivative
Primary amine
Primary alcohol
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Alcohol
Organic oxygen compound
Amine
Carbonyl group
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

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	1.59	ALOGPS
logP	0.15	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	15.9	ChemAxon
pKa (Strongest Basic)	6.26	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	92.34 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	102.34 m³·mol⁻¹	ChemAxon
Polarizability	37.18 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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
DeepCCS	[M+H]+	172.872	30932474
DeepCCS	[M-H]-	170.514	30932474
DeepCCS	[M-2H]-	203.424	30932474
DeepCCS	[M+Na]+	178.965	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	3.46 minutes	32390414
Predicted by Siyang on May 30, 2022	10.5982 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.05 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	986.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	187.4 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	108.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	148.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	62.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	296.6 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	328.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	394.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	755.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	245.9 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1080.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	248.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	264.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	334.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	267.6 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	142.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide	CC(N(CC1=CN=C(C)N=C1N)C=O)=C(CCO)SSCC=C	4284.9	Standard polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide	CC(N(CC1=CN=C(C)N=C1N)C=O)=C(CCO)SSCC=C	2937.9	Standard non polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide	CC(N(CC1=CN=C(C)N=C1N)C=O)=C(CCO)SSCC=C	3213.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,2TMS,isomer #1	C=CCSSC(CCO[Si](C)(C)C)=C(C)N(C=O)CC1=CN=C(C)N=C1N[Si](C)(C)C	3154.3	Semi standard non polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,2TMS,isomer #1	C=CCSSC(CCO[Si](C)(C)C)=C(C)N(C=O)CC1=CN=C(C)N=C1N[Si](C)(C)C	2829.3	Standard non polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,2TMS,isomer #1	C=CCSSC(CCO[Si](C)(C)C)=C(C)N(C=O)CC1=CN=C(C)N=C1N[Si](C)(C)C	4293.1	Standard polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,2TMS,isomer #2	C=CCSSC(CCO)=C(C)N(C=O)CC1=CN=C(C)N=C1N([Si](C)(C)C)[Si](C)(C)C	3052.8	Semi standard non polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,2TMS,isomer #2	C=CCSSC(CCO)=C(C)N(C=O)CC1=CN=C(C)N=C1N([Si](C)(C)C)[Si](C)(C)C	2862.2	Standard non polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,2TMS,isomer #2	C=CCSSC(CCO)=C(C)N(C=O)CC1=CN=C(C)N=C1N([Si](C)(C)C)[Si](C)(C)C	4201.2	Standard polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,3TMS,isomer #1	C=CCSSC(CCO[Si](C)(C)C)=C(C)N(C=O)CC1=CN=C(C)N=C1N([Si](C)(C)C)[Si](C)(C)C	3059.8	Semi standard non polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,3TMS,isomer #1	C=CCSSC(CCO[Si](C)(C)C)=C(C)N(C=O)CC1=CN=C(C)N=C1N([Si](C)(C)C)[Si](C)(C)C	2865.3	Standard non polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,3TMS,isomer #1	C=CCSSC(CCO[Si](C)(C)C)=C(C)N(C=O)CC1=CN=C(C)N=C1N([Si](C)(C)C)[Si](C)(C)C	3880.6	Standard polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,2TBDMS,isomer #1	C=CCSSC(CCO[Si](C)(C)C(C)(C)C)=C(C)N(C=O)CC1=CN=C(C)N=C1N[Si](C)(C)C(C)(C)C	3482.9	Semi standard non polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,2TBDMS,isomer #1	C=CCSSC(CCO[Si](C)(C)C(C)(C)C)=C(C)N(C=O)CC1=CN=C(C)N=C1N[Si](C)(C)C(C)(C)C	3233.8	Standard non polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,2TBDMS,isomer #1	C=CCSSC(CCO[Si](C)(C)C(C)(C)C)=C(C)N(C=O)CC1=CN=C(C)N=C1N[Si](C)(C)C(C)(C)C	4300.3	Standard polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,2TBDMS,isomer #2	C=CCSSC(CCO)=C(C)N(C=O)CC1=CN=C(C)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3433.2	Semi standard non polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,2TBDMS,isomer #2	C=CCSSC(CCO)=C(C)N(C=O)CC1=CN=C(C)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3279.8	Standard non polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,2TBDMS,isomer #2	C=CCSSC(CCO)=C(C)N(C=O)CC1=CN=C(C)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	4192.0	Standard polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,3TBDMS,isomer #1	C=CCSSC(CCO[Si](C)(C)C(C)(C)C)=C(C)N(C=O)CC1=CN=C(C)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3584.2	Semi standard non polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,3TBDMS,isomer #1	C=CCSSC(CCO[Si](C)(C)C(C)(C)C)=C(C)N(C=O)CC1=CN=C(C)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3445.2	Standard non polar	33892256
N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide,3TBDMS,isomer #1	C=CCSSC(CCO[Si](C)(C)C(C)(C)C)=C(C)N(C=O)CC1=CN=C(C)N=C1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3969.2	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide GC-MS (Non-derivatized) - 70eV, Positive	splash10-00dl-7933000000-603eda9df65660c5562b	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

62844202

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

172285

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]

Showing metabocard for N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide (HMDB0258148)

MOL for HMDB0258148 (N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide)

3D MOL for HMDB0258148 (N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide)

3D SDF for HMDB0258148 (N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide)

3D-SDF for HMDB0258148 (N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide)

PDB for HMDB0258148 (N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide)

3D PDB for HMDB0258148 (N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide)

SMILES for HMDB0258148 (N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide)

INCHI for HMDB0258148 (N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide)

Structure for HMDB0258148 (N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide)

3D Structure for HMDB0258148 (N-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-N-[5-hydroxy-3-(prop-2-enyldisulfanyl)pent-2-en-2-yl]formamide)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra