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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 01:31:06 UTC

Update Date

2021-09-26 22:58:28 UTC

HMDB ID

HMDB0248272

Secondary Accession Numbers

None

Metabolite Identification

Common Name

(5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid

Description

(5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. Based on a literature review very few articles have been published on (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). (5r,6s)-6-[(1r)-1-hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid 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

HMDB0248272
     RDKit          3D
(5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2....
 32 34  0  0  0  0  0  0  0  0999 V2000
   -4.0448   -0.4399   -1.5175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7305    0.9825   -1.1698 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5563    1.7490   -2.3260 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4778    1.0403   -0.3646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4884    0.3019    0.9142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3231    0.0618    1.8004 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1071   -0.0112    0.6715 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2296   -0.2985    0.9128 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6772   -0.8914    2.1960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1776   -1.2172    3.0844 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9805   -1.1263    2.5259 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0987    0.0208   -0.0130 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5531   -0.1422   -0.0827 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3878    0.9237   -0.3232 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7515    0.7878   -0.4372 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3219   -0.4609   -0.3079 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5084   -1.5075   -0.0727 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1491   -1.3775    0.0416 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1162    0.7594   -1.3501 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4605    0.0234   -0.7422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7933   -1.0551   -0.6187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3972   -0.7493   -2.3540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1150   -0.5444   -1.7947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5540    1.4195   -0.5713 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3746    1.8580   -2.8357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0104    2.0488   -0.2692 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2947   -1.9936    2.9384 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9544    1.9314   -0.4311 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4101    1.6449   -0.6291 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4008   -0.5830   -0.3962 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5263   -2.2417    0.2081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7499   -0.9136   -1.1865 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  8 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 12 19  1  0
 19 20  1  0
 20  4  1  0
 20  7  1  0
 18 13  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  0
  3 25  1  0
  4 26  1  0
 11 27  1  0
 14 28  1  0
 15 29  1  0
 16 30  1  0
 18 31  1  0
 20 32  1  0
M  END

  Mrv1652309112103312D          

 20 22  0  0  0  0            999 V2000
   -1.5279   -1.3021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7310   -1.5156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1477   -0.9323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6773   -0.9323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6773   -0.1073    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1477   -0.1073    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7310    0.4761    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620    0.1477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9469   -0.5198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620   -1.1872    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.7719   -0.5198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1844    0.1947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0094    0.1947    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4219   -0.5198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0094   -1.2343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1844   -1.2343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7169    0.9323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5239    1.1038    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1649    1.5454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5175   -2.3125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  3  6  1  0  0  0  0
  6  7  2  0  0  0  0
  5  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 11 16  1  0  0  0  0
  8 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
  2 20  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0248272

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(O)C1C2SC(=C(N2C1=O)C(O)=O)C1=CN=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C13H12N2O4S/c1-6(16)8-11(17)15-9(13(18)19)10(20-12(8)15)7-3-2-4-14-5-7/h2-6,8,12,16H,1H3,(H,18,19)

> <INCHI_KEY>
BFYPGIMLKFZWEI-UHFFFAOYSA-N

> <FORMULA>
C13H12N2O4S

> <MOLECULAR_WEIGHT>
292.31

> <EXACT_MASS>
292.051778048

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
28.637161079899478

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-(1-hydroxyethyl)-7-oxo-3-(pyridin-3-yl)-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid

> <ALOGPS_LOGP>
-0.01

> <JCHEM_LOGP>
-1.7721010845106704

> <ALOGPS_LOGS>
-1.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.89282739261757

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.033711865309218

> <JCHEM_PKA_STRONGEST_BASIC>
4.4985148080151625

> <JCHEM_POLAR_SURFACE_AREA>
90.73

> <JCHEM_REFRACTIVITY>
73.45660000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.75e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-(1-hydroxyethyl)-7-oxo-3-(pyridin-3-yl)-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0248272
     RDKit          3D
(5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2....
 32 34  0  0  0  0  0  0  0  0999 V2000
   -4.0448   -0.4399   -1.5175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7305    0.9825   -1.1698 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5563    1.7490   -2.3260 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4778    1.0403   -0.3646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4884    0.3019    0.9142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3231    0.0618    1.8004 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1071   -0.0112    0.6715 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2296   -0.2985    0.9128 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6772   -0.8914    2.1960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1776   -1.2172    3.0844 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9805   -1.1263    2.5259 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0987    0.0208   -0.0130 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5531   -0.1422   -0.0827 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3878    0.9237   -0.3232 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7515    0.7878   -0.4372 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3219   -0.4609   -0.3079 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5084   -1.5075   -0.0727 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1491   -1.3775    0.0416 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1162    0.7594   -1.3501 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4605    0.0234   -0.7422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7933   -1.0551   -0.6187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3972   -0.7493   -2.3540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1150   -0.5444   -1.7947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5540    1.4195   -0.5713 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3746    1.8580   -2.8357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0104    2.0488   -0.2692 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2947   -1.9936    2.9384 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9544    1.9314   -0.4311 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4101    1.6449   -0.6291 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4008   -0.5830   -0.3962 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5263   -2.2417    0.2081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7499   -0.9136   -1.1865 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  8 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 12 19  1  0
 19 20  1  0
 20  4  1  0
 20  7  1  0
 18 13  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  0
  3 25  1  0
  4 26  1  0
 11 27  1  0
 14 28  1  0
 15 29  1  0
 16 30  1  0
 18 31  1  0
 20 32  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0      -2.852  -2.431   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.365  -2.829   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.276  -1.740   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.264  -1.740   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       1.264  -0.200   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -0.276  -0.200   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.365   0.889   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.729   0.276   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.634  -0.970   0.000  0.00  0.00           C+0
HETATM   10  S   UNK     0       2.729  -2.216   0.000  0.00  0.00           S+0
HETATM   11  C   UNK     0       5.174  -0.970   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.944   0.363   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       7.484   0.363   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       8.254  -0.970   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.484  -2.304   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.944  -2.304   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.205   1.740   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.711   2.060   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.174   2.885   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -0.966  -4.317   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   20                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    3    7                                                  
CONECT    7    6                                                            
CONECT    8    5    9   17                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9    4                                                       
CONECT   11    9   12   16                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   11                                                       
CONECT   17    8   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20    2                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

COMPND    HMDB0248272
HETATM    1  C1  UNL     1      -4.045  -0.440  -1.517  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.730   0.982  -1.170  1.00  0.00           C  
HETATM    3  O1  UNL     1      -3.556   1.749  -2.326  1.00  0.00           O  
HETATM    4  C3  UNL     1      -2.478   1.040  -0.365  1.00  0.00           C  
HETATM    5  C4  UNL     1      -2.488   0.302   0.914  1.00  0.00           C  
HETATM    6  O2  UNL     1      -3.323   0.062   1.800  1.00  0.00           O  
HETATM    7  N1  UNL     1      -1.107  -0.011   0.671  1.00  0.00           N  
HETATM    8  C5  UNL     1       0.230  -0.299   0.913  1.00  0.00           C  
HETATM    9  C6  UNL     1       0.677  -0.891   2.196  1.00  0.00           C  
HETATM   10  O3  UNL     1      -0.178  -1.217   3.084  1.00  0.00           O  
HETATM   11  O4  UNL     1       1.981  -1.126   2.526  1.00  0.00           O  
HETATM   12  C7  UNL     1       1.099   0.021  -0.013  1.00  0.00           C  
HETATM   13  C8  UNL     1       2.553  -0.142  -0.083  1.00  0.00           C  
HETATM   14  C9  UNL     1       3.388   0.924  -0.323  1.00  0.00           C  
HETATM   15  C10 UNL     1       4.752   0.788  -0.437  1.00  0.00           C  
HETATM   16  C11 UNL     1       5.322  -0.461  -0.308  1.00  0.00           C  
HETATM   17  N2  UNL     1       4.508  -1.508  -0.073  1.00  0.00           N  
HETATM   18  C12 UNL     1       3.149  -1.377   0.042  1.00  0.00           C  
HETATM   19  S1  UNL     1       0.116   0.759  -1.350  1.00  0.00           S  
HETATM   20  C13 UNL     1      -1.461   0.023  -0.742  1.00  0.00           C  
HETATM   21  H1  UNL     1      -3.793  -1.055  -0.619  1.00  0.00           H  
HETATM   22  H2  UNL     1      -3.397  -0.749  -2.354  1.00  0.00           H  
HETATM   23  H3  UNL     1      -5.115  -0.544  -1.795  1.00  0.00           H  
HETATM   24  H4  UNL     1      -4.554   1.419  -0.571  1.00  0.00           H  
HETATM   25  H5  UNL     1      -4.375   1.858  -2.836  1.00  0.00           H  
HETATM   26  H6  UNL     1      -2.010   2.049  -0.269  1.00  0.00           H  
HETATM   27  H7  UNL     1       2.295  -1.994   2.938  1.00  0.00           H  
HETATM   28  H8  UNL     1       2.954   1.931  -0.431  1.00  0.00           H  
HETATM   29  H9  UNL     1       5.410   1.645  -0.629  1.00  0.00           H  
HETATM   30  H10 UNL     1       6.401  -0.583  -0.396  1.00  0.00           H  
HETATM   31  H11 UNL     1       2.526  -2.242   0.208  1.00  0.00           H  
HETATM   32  H12 UNL     1      -1.750  -0.914  -1.187  1.00  0.00           H  
CONECT    1    2   21   22   23
CONECT    2    3    4   24
CONECT    3   25
CONECT    4    5   20   26
CONECT    5    6    6    7
CONECT    7    8   20
CONECT    8    9   12   12
CONECT    9   10   10   11
CONECT   11   27
CONECT   12   13   19
CONECT   13   14   14   18
CONECT   14   15   28
CONECT   15   16   16   29
CONECT   16   17   30
CONECT   17   18   18
CONECT   18   31
CONECT   19   20
CONECT   20   32
END

HMDB0248272
     RDKit          3D
(5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2....
 32 34  0  0  0  0  0  0  0  0999 V2000
   -4.0448   -0.4399   -1.5175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7305    0.9825   -1.1698 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5563    1.7490   -2.3260 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4778    1.0403   -0.3646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4884    0.3019    0.9142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3231    0.0618    1.8004 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1071   -0.0112    0.6715 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2296   -0.2985    0.9128 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6772   -0.8914    2.1960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1776   -1.2172    3.0844 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9805   -1.1263    2.5259 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0987    0.0208   -0.0130 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5531   -0.1422   -0.0827 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3878    0.9237   -0.3232 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7515    0.7878   -0.4372 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3219   -0.4609   -0.3079 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5084   -1.5075   -0.0727 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1491   -1.3775    0.0416 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1162    0.7594   -1.3501 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4605    0.0234   -0.7422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7933   -1.0551   -0.6187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3972   -0.7493   -2.3540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1150   -0.5444   -1.7947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5540    1.4195   -0.5713 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3746    1.8580   -2.8357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0104    2.0488   -0.2692 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2947   -1.9936    2.9384 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9544    1.9314   -0.4311 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4101    1.6449   -0.6291 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4008   -0.5830   -0.3962 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5263   -2.2417    0.2081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7499   -0.9136   -1.1865 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  8 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 12 19  1  0
 19 20  1  0
 20  4  1  0
 20  7  1  0
 18 13  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  0
  3 25  1  0
  4 26  1  0
 11 27  1  0
 14 28  1  0
 15 29  1  0
 16 30  1  0
 18 31  1  0
 20 32  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylate	Generator

Chemical Formula

C₁₃H₁₂N₂O₄S

Average Molecular Weight

292.31

Monoisotopic Molecular Weight

292.051778048

IUPAC Name

6-(1-hydroxyethyl)-7-oxo-3-(pyridin-3-yl)-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid

Traditional Name

6-(1-hydroxyethyl)-7-oxo-3-(pyridin-3-yl)-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

CC(O)C1C2SC(=C(N2C1=O)C(O)=O)C1=CN=CC=C1

InChI Identifier

InChI=1S/C13H12N2O4S/c1-6(16)8-11(17)15-9(13(18)19)10(20-12(8)15)7-3-2-4-14-5-7/h2-6,8,12,16H,1H3,(H,18,19)

InChI Key

BFYPGIMLKFZWEI-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Penem
Thiazolecarboxylic acid or derivatives
Vinylogous thioester
Pyridine
Beta-lactam
Heteroaromatic compound
Meta-thiazoline
Thiazole
Tertiary carboxylic acid amide
Azetidine
Carboxamide group
Lactam
Thioenolether
Secondary alcohol
Carboxylic acid
Azacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Hemithioaminal
Organic nitrogen compound
Alcohol
Hydrocarbon derivative
Carbonyl group
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	-0.01	ALOGPS
logP	-1.8	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	3.03	ChemAxon
pKa (Strongest Basic)	4.5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	90.73 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	73.46 m³·mol⁻¹	ChemAxon
Polarizability	28.64 Å³	ChemAxon
Number of Rings	3	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
DeepCCS	[M+H]+	167.596	30932474
DeepCCS	[M-H]-	165.238	30932474
DeepCCS	[M-2H]-	198.124	30932474
DeepCCS	[M+Na]+	173.689	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid	CC(O)C1C2SC(=C(N2C1=O)C(O)=O)C1=CN=CC=C1	3759.5	Standard polar	33892256
(5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid	CC(O)C1C2SC(=C(N2C1=O)C(O)=O)C1=CN=CC=C1	2414.6	Standard non polar	33892256
(5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid	CC(O)C1C2SC(=C(N2C1=O)C(O)=O)C1=CN=CC=C1	2690.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-007c-9220000000-85e2d6060fae0580211c	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid 10V, Positive-QTOF	splash10-0006-0090000000-773c9cef772035e19b10	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid 20V, Positive-QTOF	splash10-004l-0090000000-f8819262ddf718414c7a	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid 40V, Positive-QTOF	splash10-0f79-2920000000-1b29c3c9483ce3e1424f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid 10V, Negative-QTOF	splash10-0006-0090000000-c14acd04ccacaa742598	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid 20V, Negative-QTOF	splash10-0w2d-0190000000-38f1e9ae1d661cc36efc	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid 40V, Negative-QTOF	splash10-0udi-5980000000-005e2835240583ef3def	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	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

14700026

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14589696

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 (5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid (HMDB0248272)

MOL for HMDB0248272 ((5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

3D MOL for HMDB0248272 ((5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

3D SDF for HMDB0248272 ((5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

3D-SDF for HMDB0248272 ((5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

PDB for HMDB0248272 ((5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

3D PDB for HMDB0248272 ((5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

SMILES for HMDB0248272 ((5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

INCHI for HMDB0248272 ((5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

Structure for HMDB0248272 ((5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

3D Structure for HMDB0248272 ((5R,6S)-6-[(1R)-1-Hydroxyethyl]-7-oxo-3-pyridin-3-yl-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra