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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 16:33:28 UTC

Update Date

2021-09-26 23:11:44 UTC

HMDB ID

HMDB0256231

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Penicillin K

Description

6-[(1-hydroxyoctylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. Based on a literature review very few articles have been published on 6-[(1-hydroxyoctylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). Penicillin k is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Penicillin K 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

HMDB0256231
     RDKit          3D
Penicillin K
 49 50  0  0  0  0  0  0  0  0999 V2000
    7.4411   -0.4771    1.3850 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7442    0.4641    0.4189 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2232    0.3711    0.6080 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8383   -1.0440    0.3323 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3581   -1.2441    0.4943 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5774   -0.3576   -0.4625 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1165   -0.6411   -0.2173 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3092    0.1992   -1.1270 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9026    0.9691   -1.9184 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0984    0.1121   -1.0794 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8645    0.9404   -1.9751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9327    0.1690   -2.6134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0565   -0.5216   -3.6402 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8046    0.5310   -1.5626 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9859    1.7004   -1.3460 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9535    1.7430    0.4834 S   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4012    0.6458    0.7510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4162    1.4487    1.5327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0317   -0.6068    1.4604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9071    0.4806   -0.6394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6027   -0.8282   -0.7171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1722   -1.6875   -1.5272 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6970   -1.1544    0.0513 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8925   -0.4323    2.3558 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4285   -1.5154    1.0053 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4788   -0.1896    1.5758 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0037    0.1381   -0.6085 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0223    1.5047    0.6114 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7735    1.0692   -0.1385 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9681    0.6096    1.6449 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1166   -1.2892   -0.7306 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3639   -1.7117    1.0365 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1091   -1.0130    1.5447 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0428   -2.2820    0.2800 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8008   -0.6271   -1.5121 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7821    0.7225   -0.2839 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8829   -0.4393    0.8484 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9669   -1.7329   -0.4111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5663   -0.5257   -0.4233 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2612    1.5861   -2.6458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2814    2.6209   -1.8306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1937    2.5396    1.4764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4598    1.2413    1.1823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3817    1.1443    2.5974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9421   -0.8035    1.5207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4236   -0.5250    2.5169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5896   -1.4476    1.0135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6455    1.2953   -0.8883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4741   -1.6179   -0.4288 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  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  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 17 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  2  0
 21 23  1  0
 15 11  1  0
 20 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  2 28  1  0
  3 29  1  0
  3 30  1  0
  4 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  6 35  1  0
  6 36  1  0
  7 37  1  0
  7 38  1  0
 10 39  1  0
 11 40  1  0
 15 41  1  0
 18 42  1  0
 18 43  1  0
 18 44  1  0
 19 45  1  0
 19 46  1  0
 19 47  1  0
 20 48  1  0
 23 49  1  0
M  END

  Mrv1533004261500422D          

 23 24  0  0  0  0            999 V2000
    2.8500   -4.8862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5644   -5.2987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2789   -4.8862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9934   -5.2987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7078   -4.8862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4223   -5.2987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1368   -4.8862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8513   -5.2987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8513   -6.1237    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5657   -4.8862    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.2802   -5.2987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0771   -5.0852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7690   -4.6358    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   11.4101   -5.1550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8595   -4.4631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1452   -5.5296    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1145   -5.9252    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2906   -5.8821    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.4937   -6.0956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0812   -6.8101    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.5638   -6.6171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3877   -6.5740    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.1893   -7.3522    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
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 14 17  1  0  0  0  0
 17 18  1  0  0  0  0
 12 18  1  0  0  0  0
 18 19  1  0  0  0  0
 11 19  1  0  0  0  0
 19 20  2  0  0  0  0
 17 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256231

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCC(=O)NC1C2SC(C)(C)C(N2C1=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H26N2O4S/c1-4-5-6-7-8-9-10(19)17-11-13(20)18-12(15(21)22)16(2,3)23-14(11)18/h11-12,14H,4-9H2,1-3H3,(H,17,19)(H,21,22)

> <INCHI_KEY>
XVASOOUVMJAZNJ-UHFFFAOYSA-N

> <FORMULA>
C16H26N2O4S

> <MOLECULAR_WEIGHT>
342.45

> <EXACT_MASS>
342.161328499

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
37.6161051803091

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3,3-dimethyl-6-octanamido-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

> <ALOGPS_LOGP>
2.97

> <JCHEM_LOGP>
2.1697173053333323

> <ALOGPS_LOGS>
-3.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.396076649400463

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6046407050420743

> <JCHEM_PKA_STRONGEST_BASIC>
-1.566400674891581

> <JCHEM_POLAR_SURFACE_AREA>
86.71000000000001

> <JCHEM_REFRACTIVITY>
87.43779999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.38e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,3-dimethyl-6-octanamido-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0256231
     RDKit          3D
Penicillin K
 49 50  0  0  0  0  0  0  0  0999 V2000
    7.4411   -0.4771    1.3850 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7442    0.4641    0.4189 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2232    0.3711    0.6080 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8383   -1.0440    0.3323 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3581   -1.2441    0.4943 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5774   -0.3576   -0.4625 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1165   -0.6411   -0.2173 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3092    0.1992   -1.1270 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9026    0.9691   -1.9184 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0984    0.1121   -1.0794 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8645    0.9404   -1.9751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9327    0.1690   -2.6134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0565   -0.5216   -3.6402 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8046    0.5310   -1.5626 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9859    1.7004   -1.3460 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9535    1.7430    0.4834 S   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4012    0.6458    0.7510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4162    1.4487    1.5327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0317   -0.6068    1.4604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9071    0.4806   -0.6394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6027   -0.8282   -0.7171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1722   -1.6875   -1.5272 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6970   -1.1544    0.0513 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8925   -0.4323    2.3558 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4285   -1.5154    1.0053 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4788   -0.1896    1.5758 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0037    0.1381   -0.6085 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0223    1.5047    0.6114 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7735    1.0692   -0.1385 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9681    0.6096    1.6449 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1166   -1.2892   -0.7306 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3639   -1.7117    1.0365 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1091   -1.0130    1.5447 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0428   -2.2820    0.2800 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8008   -0.6271   -1.5121 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7821    0.7225   -0.2839 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8829   -0.4393    0.8484 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9669   -1.7329   -0.4111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5663   -0.5257   -0.4233 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2612    1.5861   -2.6458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2814    2.6209   -1.8306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1937    2.5396    1.4764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4598    1.2413    1.1823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3817    1.1443    2.5974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9421   -0.8035    1.5207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4236   -0.5250    2.5169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5896   -1.4476    1.0135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6455    1.2953   -0.8883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4741   -1.6179   -0.4288 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  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  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 17 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  2  0
 21 23  1  0
 15 11  1  0
 20 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  2 28  1  0
  3 29  1  0
  3 30  1  0
  4 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  6 35  1  0
  6 36  1  0
  7 37  1  0
  7 38  1  0
 10 39  1  0
 11 40  1  0
 15 41  1  0
 18 42  1  0
 18 43  1  0
 18 44  1  0
 19 45  1  0
 19 46  1  0
 19 47  1  0
 20 48  1  0
 23 49  1  0
M  END

HEADER    PROTEIN                                 26-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-APR-15         0                                  
HETATM    1  C   UNK     0       5.320  -9.121   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.654  -9.891   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.987  -9.121   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.321  -9.891   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.655  -9.121   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.988  -9.891   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      13.322  -9.121   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      14.656  -9.891   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      14.656 -11.431   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      15.989  -9.121   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      17.323  -9.891   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      18.811  -9.492   0.000  0.00  0.00           C+0
HETATM   13  S   UNK     0      20.102  -8.654   0.000  0.00  0.00           S+0
HETATM   14  C   UNK     0      21.299  -9.623   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      22.138  -8.331   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      22.671 -10.322   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      20.747 -11.060   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0      19.209 -10.980   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0      17.722 -11.378   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      16.952 -12.712   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      21.586 -12.352   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      23.124 -12.271   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      20.887 -13.724   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12   19                                                  
CONECT   12   11   13   18                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16   17                                             
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   14   18   21                                                  
CONECT   18   17   12   19                                                  
CONECT   19   18   11   20                                                  
CONECT   20   19                                                            
CONECT   21   17   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

COMPND    HMDB0256231
HETATM    1  C1  UNL     1       7.441  -0.477   1.385  1.00  0.00           C  
HETATM    2  C2  UNL     1       6.744   0.464   0.419  1.00  0.00           C  
HETATM    3  C3  UNL     1       5.223   0.371   0.608  1.00  0.00           C  
HETATM    4  C4  UNL     1       4.838  -1.044   0.332  1.00  0.00           C  
HETATM    5  C5  UNL     1       3.358  -1.244   0.494  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.577  -0.358  -0.462  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.117  -0.641  -0.217  1.00  0.00           C  
HETATM    8  C8  UNL     1       0.309   0.199  -1.127  1.00  0.00           C  
HETATM    9  O1  UNL     1       0.903   0.969  -1.918  1.00  0.00           O  
HETATM   10  N1  UNL     1      -1.098   0.112  -1.079  1.00  0.00           N  
HETATM   11  C9  UNL     1      -1.864   0.940  -1.975  1.00  0.00           C  
HETATM   12  C10 UNL     1      -2.933   0.169  -2.613  1.00  0.00           C  
HETATM   13  O2  UNL     1      -3.057  -0.522  -3.640  1.00  0.00           O  
HETATM   14  N2  UNL     1      -3.805   0.531  -1.563  1.00  0.00           N  
HETATM   15  C11 UNL     1      -2.986   1.700  -1.346  1.00  0.00           C  
HETATM   16  S1  UNL     1      -2.954   1.743   0.483  1.00  0.00           S  
HETATM   17  C12 UNL     1      -4.401   0.646   0.751  1.00  0.00           C  
HETATM   18  C13 UNL     1      -5.416   1.449   1.533  1.00  0.00           C  
HETATM   19  C14 UNL     1      -4.032  -0.607   1.460  1.00  0.00           C  
HETATM   20  C15 UNL     1      -4.907   0.481  -0.639  1.00  0.00           C  
HETATM   21  C16 UNL     1      -5.603  -0.828  -0.717  1.00  0.00           C  
HETATM   22  O3  UNL     1      -5.172  -1.688  -1.527  1.00  0.00           O  
HETATM   23  O4  UNL     1      -6.697  -1.154   0.051  1.00  0.00           O  
HETATM   24  H1  UNL     1       6.893  -0.432   2.356  1.00  0.00           H  
HETATM   25  H2  UNL     1       7.428  -1.515   1.005  1.00  0.00           H  
HETATM   26  H3  UNL     1       8.479  -0.190   1.576  1.00  0.00           H  
HETATM   27  H4  UNL     1       7.004   0.138  -0.609  1.00  0.00           H  
HETATM   28  H5  UNL     1       7.022   1.505   0.611  1.00  0.00           H  
HETATM   29  H6  UNL     1       4.773   1.069  -0.139  1.00  0.00           H  
HETATM   30  H7  UNL     1       4.968   0.610   1.645  1.00  0.00           H  
HETATM   31  H8  UNL     1       5.117  -1.289  -0.731  1.00  0.00           H  
HETATM   32  H9  UNL     1       5.364  -1.712   1.037  1.00  0.00           H  
HETATM   33  H10 UNL     1       3.109  -1.013   1.545  1.00  0.00           H  
HETATM   34  H11 UNL     1       3.043  -2.282   0.280  1.00  0.00           H  
HETATM   35  H12 UNL     1       2.801  -0.627  -1.512  1.00  0.00           H  
HETATM   36  H13 UNL     1       2.782   0.722  -0.284  1.00  0.00           H  
HETATM   37  H14 UNL     1       0.883  -0.439   0.848  1.00  0.00           H  
HETATM   38  H15 UNL     1       0.967  -1.733  -0.411  1.00  0.00           H  
HETATM   39  H16 UNL     1      -1.566  -0.526  -0.423  1.00  0.00           H  
HETATM   40  H17 UNL     1      -1.261   1.586  -2.646  1.00  0.00           H  
HETATM   41  H18 UNL     1      -3.281   2.621  -1.831  1.00  0.00           H  
HETATM   42  H19 UNL     1      -5.194   2.540   1.476  1.00  0.00           H  
HETATM   43  H20 UNL     1      -6.460   1.241   1.182  1.00  0.00           H  
HETATM   44  H21 UNL     1      -5.382   1.144   2.597  1.00  0.00           H  
HETATM   45  H22 UNL     1      -2.942  -0.803   1.521  1.00  0.00           H  
HETATM   46  H23 UNL     1      -4.424  -0.525   2.517  1.00  0.00           H  
HETATM   47  H24 UNL     1      -4.590  -1.448   1.014  1.00  0.00           H  
HETATM   48  H25 UNL     1      -5.645   1.295  -0.888  1.00  0.00           H  
HETATM   49  H26 UNL     1      -7.474  -1.618  -0.429  1.00  0.00           H  
CONECT    1    2   24   25   26
CONECT    2    3   27   28
CONECT    3    4   29   30
CONECT    4    5   31   32
CONECT    5    6   33   34
CONECT    6    7   35   36
CONECT    7    8   37   38
CONECT    8    9    9   10
CONECT   10   11   39
CONECT   11   12   15   40
CONECT   12   13   13   14
CONECT   14   15   20
CONECT   15   16   41
CONECT   16   17
CONECT   17   18   19   20
CONECT   18   42   43   44
CONECT   19   45   46   47
CONECT   20   21   48
CONECT   21   22   22   23
CONECT   23   49
END

HMDB0256231
     RDKit          3D
Penicillin K
 49 50  0  0  0  0  0  0  0  0999 V2000
    7.4411   -0.4771    1.3850 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7442    0.4641    0.4189 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2232    0.3711    0.6080 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8383   -1.0440    0.3323 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3581   -1.2441    0.4943 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5774   -0.3576   -0.4625 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1165   -0.6411   -0.2173 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3092    0.1992   -1.1270 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9026    0.9691   -1.9184 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0984    0.1121   -1.0794 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8645    0.9404   -1.9751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9327    0.1690   -2.6134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0565   -0.5216   -3.6402 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8046    0.5310   -1.5626 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9859    1.7004   -1.3460 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9535    1.7430    0.4834 S   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4012    0.6458    0.7510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4162    1.4487    1.5327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0317   -0.6068    1.4604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9071    0.4806   -0.6394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6027   -0.8282   -0.7171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1722   -1.6875   -1.5272 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6970   -1.1544    0.0513 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8925   -0.4323    2.3558 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4285   -1.5154    1.0053 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4788   -0.1896    1.5758 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0037    0.1381   -0.6085 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0223    1.5047    0.6114 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7735    1.0692   -0.1385 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9681    0.6096    1.6449 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1166   -1.2892   -0.7306 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3639   -1.7117    1.0365 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1091   -1.0130    1.5447 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0428   -2.2820    0.2800 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8008   -0.6271   -1.5121 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7821    0.7225   -0.2839 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8829   -0.4393    0.8484 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9669   -1.7329   -0.4111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5663   -0.5257   -0.4233 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2612    1.5861   -2.6458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2814    2.6209   -1.8306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1937    2.5396    1.4764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4598    1.2413    1.1823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3817    1.1443    2.5974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9421   -0.8035    1.5207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4236   -0.5250    2.5169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5896   -1.4476    1.0135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6455    1.2953   -0.8883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4741   -1.6179   -0.4288 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  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  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 17 19  1  0
 17 20  1  0
 20 21  1  0
 21 22  2  0
 21 23  1  0
 15 11  1  0
 20 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  2 28  1  0
  3 29  1  0
  3 30  1  0
  4 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  6 35  1  0
  6 36  1  0
  7 37  1  0
  7 38  1  0
 10 39  1  0
 11 40  1  0
 15 41  1  0
 18 42  1  0
 18 43  1  0
 18 44  1  0
 19 45  1  0
 19 46  1  0
 19 47  1  0
 20 48  1  0
 23 49  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
6-[(1-Hydroxyoctylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate	Generator

Chemical Formula

C₁₆H₂₆N₂O₄S

Average Molecular Weight

342.45

Monoisotopic Molecular Weight

342.161328499

IUPAC Name

3,3-dimethyl-6-octanamido-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

Traditional Name

3,3-dimethyl-6-octanamido-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

CCCCCCCC(=O)NC1C2SC(C)(C)C(N2C1=O)C(O)=O

InChI Identifier

InChI=1S/C16H26N2O4S/c1-4-5-6-7-8-9-10(19)17-11-13(20)18-12(15(21)22)16(2,3)23-14(11)18/h11-12,14H,4-9H2,1-3H3,(H,17,19)(H,21,22)

InChI Key

XVASOOUVMJAZNJ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Dipeptides

Alternative Parents

Substituents

Alpha-dipeptide
Penicillin
N-acyl-alpha amino acid or derivatives
Alpha-amino acid or derivatives
Penam
Fatty amide
N-acyl-amine
Fatty acyl
Beta-lactam
Tertiary carboxylic acid amide
Thiazolidine
Azetidine
Carboxamide group
Lactam
Secondary carboxylic acid amide
Monocarboxylic acid or derivatives
Carboxylic acid
Azacycle
Organoheterocyclic compound
Dialkylthioether
Hemithioaminal
Thioether
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	2.97	ALOGPS
logP	2.17	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	3.6	ChemAxon
pKa (Strongest Basic)	-1.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	86.71 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	87.44 m³·mol⁻¹	ChemAxon
Polarizability	37.62 Å³	ChemAxon
Number of Rings	2	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]+	194.196	30932474
DeepCCS	[M-H]-	191.838	30932474
DeepCCS	[M-2H]-	224.724	30932474
DeepCCS	[M+Na]+	200.289	30932474
AllCCS	[M+H]+	178.9	32859911
AllCCS	[M+H-H2O]+	176.5	32859911
AllCCS	[M+NH4]+	181.2	32859911
AllCCS	[M+Na]+	181.8	32859911
AllCCS	[M-H]-	182.7	32859911
AllCCS	[M+Na-2H]-	183.3	32859911
AllCCS	[M+HCOO]-	184.1	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Penicillin K	CCCCCCCC(=O)NC1C2SC(C)(C)C(N2C1=O)C(O)=O	3661.8	Standard polar	33892256
Penicillin K	CCCCCCCC(=O)NC1C2SC(C)(C)C(N2C1=O)C(O)=O	2290.9	Standard non polar	33892256
Penicillin K	CCCCCCCC(=O)NC1C2SC(C)(C)C(N2C1=O)C(O)=O	2630.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Penicillin K,2TMS,isomer #1	CCCCCCCC(=O)N(C1C(=O)N2C1SC(C)(C)C2C(=O)O[Si](C)(C)C)[Si](C)(C)C	2535.5	Semi standard non polar	33892256
Penicillin K,2TMS,isomer #1	CCCCCCCC(=O)N(C1C(=O)N2C1SC(C)(C)C2C(=O)O[Si](C)(C)C)[Si](C)(C)C	2633.2	Standard non polar	33892256
Penicillin K,2TMS,isomer #1	CCCCCCCC(=O)N(C1C(=O)N2C1SC(C)(C)C2C(=O)O[Si](C)(C)C)[Si](C)(C)C	3031.5	Standard polar	33892256
Penicillin K,2TBDMS,isomer #1	CCCCCCCC(=O)N(C1C(=O)N2C1SC(C)(C)C2C(=O)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3000.2	Semi standard non polar	33892256
Penicillin K,2TBDMS,isomer #1	CCCCCCCC(=O)N(C1C(=O)N2C1SC(C)(C)C2C(=O)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3059.3	Standard non polar	33892256
Penicillin K,2TBDMS,isomer #1	CCCCCCCC(=O)N(C1C(=O)N2C1SC(C)(C)C2C(=O)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3209.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Penicillin K GC-MS (Non-derivatized) - 70eV, Positive	splash10-0563-9311000000-3cf759fb23b61942481a	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Penicillin K GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Penicillin K GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Penicillin K GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Penicillin K GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Penicillin K 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

84983

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

94167

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 Penicillin K (HMDB0256231)

MOL for HMDB0256231 (Penicillin K)

3D MOL for HMDB0256231 (Penicillin K)

3D SDF for HMDB0256231 (Penicillin K)

3D-SDF for HMDB0256231 (Penicillin K)

PDB for HMDB0256231 (Penicillin K)

3D PDB for HMDB0256231 (Penicillin K)

SMILES for HMDB0256231 (Penicillin K)

INCHI for HMDB0256231 (Penicillin K)

Structure for HMDB0256231 (Penicillin K)

3D Structure for HMDB0256231 (Penicillin K)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra