Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-23 21:02:30 UTC

Update Date

2021-09-23 21:02:30 UTC

HMDB ID

HMDB0302835

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Oryzenin

Description

Oryzenin, also known as thiamin or vitamin b1, is a member of the class of compounds known as thiamines. Thiamines are compounds containing a thiamine moiety, which is structurally characterized by a 3-[(4-Amino-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-thiazol-5-yl backbone. Oryzenin is practically insoluble (in water) and an extremely weak acidic compound (based on its pKa). Oryzenin can be found in rice, which makes oryzenin a potential biomarker for the consumption of this food product.

Structure

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

HMDB0302835
     RDKit          3D
Oryzenin
 36 36  0  0  0  0  0  0  0  0999 V2000
    5.0949    0.6949    1.3923 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8746    0.2334    0.6548 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7996    1.0300    0.5129 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6817    0.6670   -0.1377 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6405   -0.5946   -0.6887 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4253   -1.0513   -1.4225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5980    0.0321   -1.4267 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.5895    0.9115   -2.4216 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8843    1.9477   -2.0585 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4027    1.1991   -0.6107 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5495    1.5787    0.2878 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7635    0.7478    0.0946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5380   -0.5825    0.3370 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5179    0.1622   -0.4895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5874   -0.7971    0.6992 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7068   -1.4175   -0.5617 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7020   -2.6216   -1.0720 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -0.9839    0.1049 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Cl  0  0  0  0  0 15  0  0  0  0  0  0
    5.1224    1.8073    1.2730 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1103    0.3561    2.4272 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0284    0.3261    0.9072 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8234    1.3508   -0.2303 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7103   -1.3240   -2.4330 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0319   -1.9335   -0.8607 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0974    0.9630   -3.2871 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2307    1.5560    1.3323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7860    2.6474    0.0539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1804    0.9232   -0.9328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5673    1.0739    0.8051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2539   -1.1722    0.0070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5349   -1.0879    0.9728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0814   -1.7375    0.4316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0989   -0.3240    1.5251 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8902   -2.9772   -1.5832 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6313   -1.6038    0.2161 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 10 14  2  0
 14 15  1  0
  5 16  1  0
 16 17  2  3
 16 18  1  0
 18  2  1  0
 14  7  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  6 24  1  0
  6 25  1  0
  8 26  1  0
 11 27  1  0
 11 28  1  0
 12 29  1  0
 12 30  1  0
 13 31  1  0
 15 32  1  0
 15 33  1  0
 15 34  1  0
 17 35  1  0
 18 36  1  0
M  CHG  2   7   1  19  -1
M  END


  Mrv1652305221920122D          

 19 19  0  0  0  0            999 V2000
   -1.8182   -0.4053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4918    2.2997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2635   -2.1123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0840   -2.0260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3483    1.8872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3661    0.6497    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3013   -0.6602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0336   -0.6602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7773    1.8872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3483    1.0622    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7786   -1.4448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0628    0.6497    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0628   -0.1753    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0628    2.2997    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7773    1.0622    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3661   -0.1753    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -2.5690   -2.6935    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0464   -1.4448    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.8489    0.0000    0.0000 Cl  0  5  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  8  1  1  0  0  0  0
  9  2  1  0  0  0  0
 10  5  2  0  0  0  0
 10  6  1  0  0  0  0
 11  3  1  0  0  0  0
 11  8  2  0  0  0  0
 12 10  1  0  0  0  0
 13 12  2  0  0  0  0
 14  5  1  0  0  0  0
 14  9  2  0  0  0  0
 15  9  1  0  0  0  0
 15 12  1  0  0  0  0
 16  6  1  0  0  0  0
 16  7  2  0  0  0  0
 16  8  1  0  0  0  0
 17  4  1  0  0  0  0
 18  7  1  0  0  0  0
 18 11  1  0  0  0  0
M  CHG  2  16   1  19  -1
M  END
> <DATABASE_ID>
HMDB0302835

> <DATABASE_NAME>
hmdb

> <SMILES>
[Cl-].CC1=C(CCO)SC=[N+]1CC1=CN=C(C)NC1=N

> <INCHI_IDENTIFIER>
InChI=1S/C12H17N4OS.ClH/c1-8-11(3-4-17)18-7-16(8)6-10-5-14-9(2)15-12(10)13;/h5,7,17H,3-4,6H2,1-2H3,(H2,13,14,15);1H/q+1;/p-1

> <INCHI_KEY>
MYVIATVLJGTBFV-UHFFFAOYSA-M

> <FORMULA>
C12H17ClN4OS

> <MOLECULAR_WEIGHT>
300.808

> <EXACT_MASS>
300.081159583

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
28.09003819938581

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-(2-hydroxyethyl)-3-[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium chloride

> <ALOGPS_LOGP>
-1.89

> <JCHEM_LOGP>
-3.831396973138412

> <ALOGPS_LOGS>
-4.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.252591931637426

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.35818631653136

> <JCHEM_PKA_STRONGEST_BASIC>
2.142301599938134

> <JCHEM_POLAR_SURFACE_AREA>
72.35000000000001

> <JCHEM_REFRACTIVITY>
82.17669999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.57e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β-amin chloride

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0302835
     RDKit          3D
Oryzenin
 36 36  0  0  0  0  0  0  0  0999 V2000
    5.0949    0.6949    1.3923 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8746    0.2334    0.6548 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7996    1.0300    0.5129 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6817    0.6670   -0.1377 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6405   -0.5946   -0.6887 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4253   -1.0513   -1.4225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5980    0.0321   -1.4267 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.5895    0.9115   -2.4216 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8843    1.9477   -2.0585 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4027    1.1991   -0.6107 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5495    1.5787    0.2878 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7635    0.7478    0.0946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5380   -0.5825    0.3370 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5179    0.1622   -0.4895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5874   -0.7971    0.6992 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7068   -1.4175   -0.5617 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7020   -2.6216   -1.0720 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -0.9839    0.1049 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Cl  0  0  0  0  0 15  0  0  0  0  0  0
    5.1224    1.8073    1.2730 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1103    0.3561    2.4272 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0284    0.3261    0.9072 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8234    1.3508   -0.2303 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7103   -1.3240   -2.4330 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0319   -1.9335   -0.8607 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0974    0.9630   -3.2871 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2307    1.5560    1.3323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7860    2.6474    0.0539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1804    0.9232   -0.9328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5673    1.0739    0.8051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2539   -1.1722    0.0070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5349   -1.0879    0.9728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0814   -1.7375    0.4316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0989   -0.3240    1.5251 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8902   -2.9772   -1.5832 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6313   -1.6038    0.2161 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 10 14  2  0
 14 15  1  0
  5 16  1  0
 16 17  2  3
 16 18  1  0
 18  2  1  0
 14  7  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  6 24  1  0
  6 25  1  0
  8 26  1  0
 11 27  1  0
 11 28  1  0
 12 29  1  0
 12 30  1  0
 13 31  1  0
 15 32  1  0
 15 33  1  0
 15 34  1  0
 17 35  1  0
 18 36  1  0
M  CHG  2   7   1  19  -1
M  END

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0      -3.394  -0.757   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.651   4.293   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.359  -3.943   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.890  -3.782   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.650   3.523   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.683   1.213   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.562  -1.232   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.929  -1.232   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.318   3.523   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.650   1.983   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.453  -2.697   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.984   1.213   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       1.984  -0.327   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       1.984   4.293   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       3.318   1.983   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      -0.683  -0.327   0.000  0.00  0.00           N+1
HETATM   17  O   UNK     0      -4.795  -5.028   0.000  0.00  0.00           O+0
HETATM   18  S   UNK     0       0.087  -2.697   0.000  0.00  0.00           S+0
HETATM   19 Cl   UNK     0       9.051   0.000   0.000  0.00  0.00          Cl-1
CONECT    1    8                                                            
CONECT    2    9                                                            
CONECT    3    4   11                                                       
CONECT    4    3   17                                                       
CONECT    5   10   14                                                       
CONECT    6   10   16                                                       
CONECT    7   16   18                                                       
CONECT    8    1   11   16                                                  
CONECT    9    2   14   15                                                  
CONECT   10    5    6   12                                                  
CONECT   11    3    8   18                                                  
CONECT   12   10   13   15                                                  
CONECT   13   12                                                            
CONECT   14    5    9                                                       
CONECT   15    9   12                                                       
CONECT   16    6    7    8                                                  
CONECT   17    4                                                            
CONECT   18    7   11                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

COMPND    HMDB0302835
HETATM    1  C1  UNL     1       5.095   0.695   1.392  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.875   0.233   0.655  1.00  0.00           C  
HETATM    3  N1  UNL     1       2.800   1.030   0.513  1.00  0.00           N  
HETATM    4  C3  UNL     1       1.682   0.667  -0.138  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.641  -0.595  -0.689  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.425  -1.051  -1.422  1.00  0.00           C  
HETATM    7  N2  UNL     1      -0.598   0.032  -1.427  1.00  0.00           N1+
HETATM    8  C6  UNL     1      -0.590   0.912  -2.422  1.00  0.00           C  
HETATM    9  S1  UNL     1      -1.884   1.948  -2.058  1.00  0.00           S  
HETATM   10  C7  UNL     1      -2.403   1.199  -0.611  1.00  0.00           C  
HETATM   11  C8  UNL     1      -3.550   1.579   0.288  1.00  0.00           C  
HETATM   12  C9  UNL     1      -4.763   0.748   0.095  1.00  0.00           C  
HETATM   13  O1  UNL     1      -4.538  -0.583   0.337  1.00  0.00           O  
HETATM   14  C10 UNL     1      -1.518   0.162  -0.489  1.00  0.00           C  
HETATM   15  C11 UNL     1      -1.587  -0.797   0.699  1.00  0.00           C  
HETATM   16  C12 UNL     1       2.707  -1.417  -0.562  1.00  0.00           C  
HETATM   17  N3  UNL     1       2.702  -2.622  -1.072  1.00  0.00           N  
HETATM   18  N4  UNL     1       3.793  -0.984   0.105  1.00  0.00           N  
HETATM   19 CL1  UNL     1       0.000   0.000   0.000  1.00  0.00          CL1-
HETATM   20  H1  UNL     1       5.122   1.807   1.273  1.00  0.00           H  
HETATM   21  H2  UNL     1       5.110   0.356   2.427  1.00  0.00           H  
HETATM   22  H3  UNL     1       6.028   0.326   0.907  1.00  0.00           H  
HETATM   23  H4  UNL     1       0.823   1.351  -0.230  1.00  0.00           H  
HETATM   24  H5  UNL     1       0.710  -1.324  -2.433  1.00  0.00           H  
HETATM   25  H6  UNL     1       0.032  -1.933  -0.861  1.00  0.00           H  
HETATM   26  H7  UNL     1       0.097   0.963  -3.287  1.00  0.00           H  
HETATM   27  H8  UNL     1      -3.231   1.556   1.332  1.00  0.00           H  
HETATM   28  H9  UNL     1      -3.786   2.647   0.054  1.00  0.00           H  
HETATM   29  H10 UNL     1      -5.180   0.923  -0.933  1.00  0.00           H  
HETATM   30  H11 UNL     1      -5.567   1.074   0.805  1.00  0.00           H  
HETATM   31  H12 UNL     1      -5.254  -1.172   0.007  1.00  0.00           H  
HETATM   32  H13 UNL     1      -0.535  -1.088   0.973  1.00  0.00           H  
HETATM   33  H14 UNL     1      -2.081  -1.738   0.432  1.00  0.00           H  
HETATM   34  H15 UNL     1      -2.099  -0.324   1.525  1.00  0.00           H  
HETATM   35  H16 UNL     1       1.890  -2.977  -1.583  1.00  0.00           H  
HETATM   36  H17 UNL     1       4.631  -1.604   0.216  1.00  0.00           H  
CONECT    1    2   20   21   22
CONECT    2    3    3   18
CONECT    3    4
CONECT    4    5    5   23
CONECT    5    6   16
CONECT    6    7   24   25
CONECT    7    8    8   14
CONECT    8    9   26
CONECT    9   10
CONECT   10   11   14   14
CONECT   11   12   27   28
CONECT   12   13   29   30
CONECT   13   31
CONECT   14   15
CONECT   15   32   33   34
CONECT   16   17   17   18
CONECT   17   35
CONECT   18   36
END

HMDB0302835
     RDKit          3D
Oryzenin
 36 36  0  0  0  0  0  0  0  0999 V2000
    5.0949    0.6949    1.3923 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8746    0.2334    0.6548 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7996    1.0300    0.5129 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6817    0.6670   -0.1377 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6405   -0.5946   -0.6887 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4253   -1.0513   -1.4225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5980    0.0321   -1.4267 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.5895    0.9115   -2.4216 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8843    1.9477   -2.0585 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4027    1.1991   -0.6107 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5495    1.5787    0.2878 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7635    0.7478    0.0946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5380   -0.5825    0.3370 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5179    0.1622   -0.4895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5874   -0.7971    0.6992 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7068   -1.4175   -0.5617 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7020   -2.6216   -1.0720 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -0.9839    0.1049 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Cl  0  0  0  0  0 15  0  0  0  0  0  0
    5.1224    1.8073    1.2730 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1103    0.3561    2.4272 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0284    0.3261    0.9072 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8234    1.3508   -0.2303 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7103   -1.3240   -2.4330 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0319   -1.9335   -0.8607 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0974    0.9630   -3.2871 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2307    1.5560    1.3323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7860    2.6474    0.0539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1804    0.9232   -0.9328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5673    1.0739    0.8051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2539   -1.1722    0.0070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5349   -1.0879    0.9728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0814   -1.7375    0.4316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0989   -0.3240    1.5251 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8902   -2.9772   -1.5832 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6313   -1.6038    0.2161 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 10 14  2  0
 14 15  1  0
  5 16  1  0
 16 17  2  3
 16 18  1  0
 18  2  1  0
 14  7  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  6 24  1  0
  6 25  1  0
  8 26  1  0
 11 27  1  0
 11 28  1  0
 12 29  1  0
 12 30  1  0
 13 31  1  0
 15 32  1  0
 15 33  1  0
 15 34  1  0
 17 35  1  0
 18 36  1  0
M  CHG  2   7   1  19  -1
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3-[(4-Amino-2-methyl-5-pyrimidinyl)methyl]-5-(2-hydroxyethyl)-4-methylthiazolium chloride	ChEBI
Thiamin	ChEBI
Thiamine	ChEBI
Thiamine chloride	ChEBI
Thiamine monochloride	ChEBI
Thiaminum	ChEBI
Tiamina	ChEBI
Vitamin b1	ChEBI

Chemical Formula

C₁₂H₁₇ClN₄OS

Average Molecular Weight

300.808

Monoisotopic Molecular Weight

300.081159583

IUPAC Name

5-(2-hydroxyethyl)-3-[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium chloride

Traditional Name

β-amin chloride

CAS Registry Number

Not Available

SMILES

[Cl-].CC1=C(CCO)SC=[N+]1CC1=CN=C(C)NC1=N

InChI Identifier

InChI=1S/C12H17N4OS.ClH/c1-8-11(3-4-17)18-7-16(8)6-10-5-14-9(2)15-12(10)13;/h5,7,17H,3-4,6H2,1-2H3,(H2,13,14,15);1H/q+1;/p-1

InChI Key

MYVIATVLJGTBFV-UHFFFAOYSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as thiamines. Thiamines are compounds containing a thiamine moiety, which is structurally characterized by a 3-[(4-Amino-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-thiazol-5-yl backbone.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Thiamines

Alternative Parents

Substituents

Thiamine
4,5-disubstituted 1,3-thiazole
Aminopyrimidine
Imidolactam
Azole
Thiazole
Heteroaromatic compound
Azacycle
Hydrocarbon derivative
Organic salt
Alcohol
Organopnictogen compound
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Organic oxygen compound
Organic chloride salt
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

thiamine (CHEBI:33283 )

Ontology

Not Available

Exogenous (HMDB: HMDB0302835)

Food

Cereal and cereal product

Cereal

Rice (FooDB: FOOD00125)

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	-1.9	ALOGPS
logP	-3.8	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	8.36	ChemAxon
pKa (Strongest Basic)	2.14	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	72.35 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	82.18 m³·mol⁻¹	ChemAxon
Polarizability	28.09 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]+	190.083	32859911
AllCCS	[M+H-H2O]+	187.29	32859911
AllCCS	[M+Na]+	193.401	32859911
AllCCS	[M+NH4]+	192.662	32859911
AllCCS	[M-H]-	167.61	32859911
AllCCS	[M+Na-2H]-	168.173	32859911
AllCCS	[M+HCOO]-	168.904	32859911
DeepCCS	[M+H]+	165.23	30932474
DeepCCS	[M-H]-	162.845	30932474
DeepCCS	[M-2H]-	195.917	30932474
DeepCCS	[M+Na]+	171.296	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	430.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	227.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	74.9 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	161.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	41.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	286.7 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	248.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	790.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	567.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	41.6 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	632.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	179.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	202.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	544.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	586.4 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	402.7 seconds	40023050

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Oryzenin,2TMS,isomer #1	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C)=C2C)C(=N[Si](C)(C)C)[NH]1	2354.1	Semi standard non polar	33892256
Oryzenin,2TMS,isomer #1	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C)=C2C)C(=N[Si](C)(C)C)[NH]1	2532.0	Standard non polar	33892256
Oryzenin,2TMS,isomer #1	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C)=C2C)C(=N[Si](C)(C)C)[NH]1	3308.6	Standard polar	33892256
Oryzenin,2TMS,isomer #2	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C)=C2C)C(=N)N1[Si](C)(C)C	2497.0	Semi standard non polar	33892256
Oryzenin,2TMS,isomer #2	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C)=C2C)C(=N)N1[Si](C)(C)C	2579.7	Standard non polar	33892256
Oryzenin,2TMS,isomer #2	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C)=C2C)C(=N)N1[Si](C)(C)C	3327.6	Standard polar	33892256
Oryzenin,2TMS,isomer #3	CC1=NC=C(C[N+]2=CSC(CCO)=C2C)C(=N[Si](C)(C)C)N1[Si](C)(C)C	2526.4	Semi standard non polar	33892256
Oryzenin,2TMS,isomer #3	CC1=NC=C(C[N+]2=CSC(CCO)=C2C)C(=N[Si](C)(C)C)N1[Si](C)(C)C	2571.2	Standard non polar	33892256
Oryzenin,2TMS,isomer #3	CC1=NC=C(C[N+]2=CSC(CCO)=C2C)C(=N[Si](C)(C)C)N1[Si](C)(C)C	3243.5	Standard polar	33892256
Oryzenin,3TMS,isomer #1	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C)=C2C)C(=N[Si](C)(C)C)N1[Si](C)(C)C	2512.5	Semi standard non polar	33892256
Oryzenin,3TMS,isomer #1	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C)=C2C)C(=N[Si](C)(C)C)N1[Si](C)(C)C	2625.1	Standard non polar	33892256
Oryzenin,3TMS,isomer #1	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C)=C2C)C(=N[Si](C)(C)C)N1[Si](C)(C)C	3019.7	Standard polar	33892256
Oryzenin,2TBDMS,isomer #1	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C(C)(C)C)=C2C)C(=N[Si](C)(C)C(C)(C)C)[NH]1	2781.6	Semi standard non polar	33892256
Oryzenin,2TBDMS,isomer #1	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C(C)(C)C)=C2C)C(=N[Si](C)(C)C(C)(C)C)[NH]1	2946.1	Standard non polar	33892256
Oryzenin,2TBDMS,isomer #1	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C(C)(C)C)=C2C)C(=N[Si](C)(C)C(C)(C)C)[NH]1	3401.0	Standard polar	33892256
Oryzenin,2TBDMS,isomer #2	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C(C)(C)C)=C2C)C(=N)N1[Si](C)(C)C(C)(C)C	2945.5	Semi standard non polar	33892256
Oryzenin,2TBDMS,isomer #2	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C(C)(C)C)=C2C)C(=N)N1[Si](C)(C)C(C)(C)C	2999.0	Standard non polar	33892256
Oryzenin,2TBDMS,isomer #2	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C(C)(C)C)=C2C)C(=N)N1[Si](C)(C)C(C)(C)C	3358.2	Standard polar	33892256
Oryzenin,2TBDMS,isomer #3	CC1=NC=C(C[N+]2=CSC(CCO)=C2C)C(=N[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	2943.8	Semi standard non polar	33892256
Oryzenin,2TBDMS,isomer #3	CC1=NC=C(C[N+]2=CSC(CCO)=C2C)C(=N[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	2986.8	Standard non polar	33892256
Oryzenin,2TBDMS,isomer #3	CC1=NC=C(C[N+]2=CSC(CCO)=C2C)C(=N[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	3286.2	Standard polar	33892256
Oryzenin,3TBDMS,isomer #1	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C(C)(C)C)=C2C)C(=N[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	3124.6	Semi standard non polar	33892256
Oryzenin,3TBDMS,isomer #1	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C(C)(C)C)=C2C)C(=N[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	3232.2	Standard non polar	33892256
Oryzenin,3TBDMS,isomer #1	CC1=NC=C(C[N+]2=CSC(CCO[Si](C)(C)C(C)(C)C)=C2C)C(=N[Si](C)(C)C(C)(C)C)N1[Si](C)(C)C(C)(C)C	3226.3	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 - Oryzenin 10V, Positive-QTOF	splash10-0udi-0009000000-cd32abfed76b69866da8	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Oryzenin 20V, Positive-QTOF	splash10-0udi-0009000000-cd32abfed76b69866da8	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Oryzenin 40V, Positive-QTOF	splash10-0udi-0009000000-cd32abfed76b69866da8	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Oryzenin 10V, Negative-QTOF	splash10-0002-0090000000-a7fcf2f90dad919c8b5e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Oryzenin 20V, Negative-QTOF	splash10-0002-0090000000-a7fcf2f90dad919c8b5e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Oryzenin 40V, Negative-QTOF	splash10-0002-0090000000-a7fcf2f90dad919c8b5e	2016-08-03	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

FDB006415

KNApSAcK ID

C00000775

Chemspider ID

5819

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Thiamine

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

33283

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1389481

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for Oryzenin (HMDB0302835)

MOL for HMDB0302835 (Oryzenin)

3D MOL for HMDB0302835 (Oryzenin)

3D SDF for HMDB0302835 (Oryzenin)

3D-SDF for HMDB0302835 (Oryzenin)

PDB for HMDB0302835 (Oryzenin)

3D PDB for HMDB0302835 (Oryzenin)

SMILES for HMDB0302835 (Oryzenin)

INCHI for HMDB0302835 (Oryzenin)

Structure for HMDB0302835 (Oryzenin)

3D Structure for HMDB0302835 (Oryzenin)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Derivatized

MS/MS Spectra