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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 16:33:25 UTC

Update Date

2021-09-26 23:11:44 UTC

HMDB ID

HMDB0256230

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Penicillin F

Description

6-[(1-hydroxyhex-3-en-1-ylidene)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 n-acyl-alpha amino acids and derivatives. N-acyl-alpha amino acids and derivatives are compounds containing an alpha amino acid (or a derivative thereof) which bears an acyl group at its terminal nitrogen atom. Based on a literature review very few articles have been published on 6-[(1-hydroxyhex-3-en-1-ylidene)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 f is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Penicillin F 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

HMDB0256230
     RDKit          3D
Penicillin F
 41 42  0  0  0  0  0  0  0  0999 V2000
    5.5846   -1.4703   -1.1369 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5319   -0.0154   -0.6424 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3586    0.0078    0.8252 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3404    0.5676    1.4484 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1944    1.2679    0.8268 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9539    0.5243    1.2364 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0073   -0.5030    1.9828 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7132    1.0076    0.7608 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5313    0.3486    1.1089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6004    1.3280    1.5228 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5479    2.2171    2.4158 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5137    0.8246    0.5705 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3999    0.2133   -0.1143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1055   -1.4685   -0.3368 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8593   -0.9760   -0.2617 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4902   -1.3780   -1.5615 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5562   -1.5623    0.9354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7356    0.5339   -0.1260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7559    1.2427   -1.4047 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7291    1.1035   -2.1761 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7192    2.0673   -1.7814 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5490   -1.7786   -1.3388 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0773   -2.0342   -0.3251 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1685   -1.4483   -2.0704 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6972    0.4662   -1.1618 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5138    0.4433   -0.8931 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1537   -0.4869    1.4272 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3814    0.4850    2.5565 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2242    1.3492   -0.2628 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1017    2.2772    1.2971 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6871    1.8473    0.1524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4353   -0.5269    1.7505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0325    0.6698   -1.0266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8320   -1.0421   -2.3844 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5371   -1.0297   -1.6771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4372   -2.5041   -1.5934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8445   -2.1786    1.5006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3844   -2.2233    0.6131 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9867   -0.8080    1.6034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6197    0.8530    0.4835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5848    2.3501   -2.7430 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 15 18  1  0
 18 19  1  0
 19 20  2  0
 19 21  1  0
 13  9  1  0
 18 12  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  8 31  1  0
  9 32  1  0
 13 33  1  0
 16 34  1  0
 16 35  1  0
 16 36  1  0
 17 37  1  0
 17 38  1  0
 17 39  1  0
 18 40  1  0
 21 41  1  0
M  END

  Mrv1533004201503082D          

 21 22  0  0  0  0            999 V2000
   -3.7758    1.9417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1925    1.3583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3956    1.5719    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8122    0.9885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0153    1.2020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4319    0.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6455   -0.1782    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3649    0.8322    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483    0.2488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7733    0.2488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5579    0.5038    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.0428   -0.1637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6559    0.3884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6559   -0.7157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5579   -0.8311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7733   -0.5762    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483   -0.5762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3649   -1.1595    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8129   -1.6157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6198   -1.7873    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2608   -2.2288    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  4  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 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
 12 14  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
 10 16  1  0  0  0  0
 16 17  1  0  0  0  0
  9 17  1  0  0  0  0
 17 18  2  0  0  0  0
 15 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256230

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C14H20N2O4S/c1-4-5-6-7-8(17)15-9-11(18)16-10(13(19)20)14(2,3)21-12(9)16/h5-6,9-10,12H,4,7H2,1-3H3,(H,15,17)(H,19,20)

> <INCHI_KEY>
QRLCJUNAKLMRGP-UHFFFAOYSA-N

> <FORMULA>
C14H20N2O4S

> <MOLECULAR_WEIGHT>
312.38

> <EXACT_MASS>
312.114378306

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
32.23764367504215

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
2.12

> <JCHEM_LOGP>
0.9186583186666665

> <ALOGPS_LOGS>
-2.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.22269167287283

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6214312733597867

> <JCHEM_PKA_STRONGEST_BASIC>
-2.0382503634200098

> <JCHEM_POLAR_SURFACE_AREA>
86.71000000000001

> <JCHEM_REFRACTIVITY>
79.35239999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.18e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0256230
     RDKit          3D
Penicillin F
 41 42  0  0  0  0  0  0  0  0999 V2000
    5.5846   -1.4703   -1.1369 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5319   -0.0154   -0.6424 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3586    0.0078    0.8252 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3404    0.5676    1.4484 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1944    1.2679    0.8268 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9539    0.5243    1.2364 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0073   -0.5030    1.9828 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7132    1.0076    0.7608 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5313    0.3486    1.1089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6004    1.3280    1.5228 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5479    2.2171    2.4158 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5137    0.8246    0.5705 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3999    0.2133   -0.1143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1055   -1.4685   -0.3368 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8593   -0.9760   -0.2617 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4902   -1.3780   -1.5615 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5562   -1.5623    0.9354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7356    0.5339   -0.1260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7559    1.2427   -1.4047 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7291    1.1035   -2.1761 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7192    2.0673   -1.7814 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5490   -1.7786   -1.3388 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0773   -2.0342   -0.3251 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1685   -1.4483   -2.0704 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6972    0.4662   -1.1618 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5138    0.4433   -0.8931 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1537   -0.4869    1.4272 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3814    0.4850    2.5565 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2242    1.3492   -0.2628 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1017    2.2772    1.2971 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6871    1.8473    0.1524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4353   -0.5269    1.7505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0325    0.6698   -1.0266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8320   -1.0421   -2.3844 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5371   -1.0297   -1.6771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4372   -2.5041   -1.5934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8445   -2.1786    1.5006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3844   -2.2233    0.6131 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9867   -0.8080    1.6034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6197    0.8530    0.4835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5848    2.3501   -2.7430 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 15 18  1  0
 18 19  1  0
 19 20  2  0
 19 21  1  0
 13  9  1  0
 18 12  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  8 31  1  0
  9 32  1  0
 13 33  1  0
 16 34  1  0
 16 35  1  0
 16 36  1  0
 17 37  1  0
 17 38  1  0
 17 39  1  0
 18 40  1  0
 21 41  1  0
M  END

HEADER    PROTEIN                                 20-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-15         0                                  
HETATM    1  C   UNK     0      -7.048   3.624   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.959   2.536   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.472   2.934   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.383   1.845   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.895   2.244   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.806   1.155   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.205  -0.333   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       0.681   1.553   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       1.770   0.464   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.310   0.464   0.000  0.00  0.00           C+0
HETATM   11  S   UNK     0       4.775   0.940   0.000  0.00  0.00           S+0
HETATM   12  C   UNK     0       5.680  -0.306   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.824   0.725   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.824  -1.336   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.775  -1.551   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       3.310  -1.076   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       1.770  -1.076   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.681  -2.164   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       5.251  -3.016   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       6.757  -3.336   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       4.220  -4.160   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    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   17                                                  
CONECT   10    9   11   16                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14   15                                             
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   12   16   19                                                  
CONECT   16   15   10   17                                                  
CONECT   17   16    9   18                                                  
CONECT   18   17                                                            
CONECT   19   15   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

COMPND    HMDB0256230
HETATM    1  C1  UNL     1       5.585  -1.470  -1.137  1.00  0.00           C  
HETATM    2  C2  UNL     1       5.532  -0.015  -0.642  1.00  0.00           C  
HETATM    3  C3  UNL     1       5.359   0.008   0.825  1.00  0.00           C  
HETATM    4  C4  UNL     1       4.340   0.568   1.448  1.00  0.00           C  
HETATM    5  C5  UNL     1       3.194   1.268   0.827  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.954   0.524   1.236  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.007  -0.503   1.983  1.00  0.00           O  
HETATM    8  N1  UNL     1       0.713   1.008   0.761  1.00  0.00           N  
HETATM    9  C7  UNL     1      -0.531   0.349   1.109  1.00  0.00           C  
HETATM   10  C8  UNL     1      -1.600   1.328   1.523  1.00  0.00           C  
HETATM   11  O2  UNL     1      -1.548   2.217   2.416  1.00  0.00           O  
HETATM   12  N2  UNL     1      -2.514   0.825   0.570  1.00  0.00           N  
HETATM   13  C9  UNL     1      -1.400   0.213  -0.114  1.00  0.00           C  
HETATM   14  S1  UNL     1      -2.105  -1.469  -0.337  1.00  0.00           S  
HETATM   15  C10 UNL     1      -3.859  -0.976  -0.262  1.00  0.00           C  
HETATM   16  C11 UNL     1      -4.490  -1.378  -1.562  1.00  0.00           C  
HETATM   17  C12 UNL     1      -4.556  -1.562   0.935  1.00  0.00           C  
HETATM   18  C13 UNL     1      -3.736   0.534  -0.126  1.00  0.00           C  
HETATM   19  C14 UNL     1      -3.756   1.243  -1.405  1.00  0.00           C  
HETATM   20  O3  UNL     1      -4.729   1.103  -2.176  1.00  0.00           O  
HETATM   21  O4  UNL     1      -2.719   2.067  -1.781  1.00  0.00           O  
HETATM   22  H1  UNL     1       4.549  -1.779  -1.339  1.00  0.00           H  
HETATM   23  H2  UNL     1       6.077  -2.034  -0.325  1.00  0.00           H  
HETATM   24  H3  UNL     1       6.169  -1.448  -2.070  1.00  0.00           H  
HETATM   25  H4  UNL     1       4.697   0.466  -1.162  1.00  0.00           H  
HETATM   26  H5  UNL     1       6.514   0.443  -0.893  1.00  0.00           H  
HETATM   27  H6  UNL     1       6.154  -0.487   1.427  1.00  0.00           H  
HETATM   28  H7  UNL     1       4.381   0.485   2.556  1.00  0.00           H  
HETATM   29  H8  UNL     1       3.224   1.349  -0.263  1.00  0.00           H  
HETATM   30  H9  UNL     1       3.102   2.277   1.297  1.00  0.00           H  
HETATM   31  H10 UNL     1       0.687   1.847   0.152  1.00  0.00           H  
HETATM   32  H11 UNL     1      -0.435  -0.527   1.750  1.00  0.00           H  
HETATM   33  H12 UNL     1      -1.032   0.670  -1.027  1.00  0.00           H  
HETATM   34  H13 UNL     1      -3.832  -1.042  -2.384  1.00  0.00           H  
HETATM   35  H14 UNL     1      -5.537  -1.030  -1.677  1.00  0.00           H  
HETATM   36  H15 UNL     1      -4.437  -2.504  -1.593  1.00  0.00           H  
HETATM   37  H16 UNL     1      -3.844  -2.179   1.501  1.00  0.00           H  
HETATM   38  H17 UNL     1      -5.384  -2.223   0.613  1.00  0.00           H  
HETATM   39  H18 UNL     1      -4.987  -0.808   1.603  1.00  0.00           H  
HETATM   40  H19 UNL     1      -4.620   0.853   0.483  1.00  0.00           H  
HETATM   41  H20 UNL     1      -2.585   2.350  -2.743  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3   25   26
CONECT    3    4    4   27
CONECT    4    5   28
CONECT    5    6   29   30
CONECT    6    7    7    8
CONECT    8    9   31
CONECT    9   10   13   32
CONECT   10   11   11   12
CONECT   12   13   18
CONECT   13   14   33
CONECT   14   15
CONECT   15   16   17   18
CONECT   16   34   35   36
CONECT   17   37   38   39
CONECT   18   19   40
CONECT   19   20   20   21
CONECT   21   41
END

HMDB0256230
     RDKit          3D
Penicillin F
 41 42  0  0  0  0  0  0  0  0999 V2000
    5.5846   -1.4703   -1.1369 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5319   -0.0154   -0.6424 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3586    0.0078    0.8252 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3404    0.5676    1.4484 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1944    1.2679    0.8268 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9539    0.5243    1.2364 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0073   -0.5030    1.9828 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7132    1.0076    0.7608 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5313    0.3486    1.1089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6004    1.3280    1.5228 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5479    2.2171    2.4158 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5137    0.8246    0.5705 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3999    0.2133   -0.1143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1055   -1.4685   -0.3368 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8593   -0.9760   -0.2617 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4902   -1.3780   -1.5615 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5562   -1.5623    0.9354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7356    0.5339   -0.1260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7559    1.2427   -1.4047 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7291    1.1035   -2.1761 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7192    2.0673   -1.7814 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5490   -1.7786   -1.3388 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0773   -2.0342   -0.3251 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1685   -1.4483   -2.0704 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6972    0.4662   -1.1618 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5138    0.4433   -0.8931 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1537   -0.4869    1.4272 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3814    0.4850    2.5565 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2242    1.3492   -0.2628 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1017    2.2772    1.2971 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6871    1.8473    0.1524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4353   -0.5269    1.7505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0325    0.6698   -1.0266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8320   -1.0421   -2.3844 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5371   -1.0297   -1.6771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4372   -2.5041   -1.5934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8445   -2.1786    1.5006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3844   -2.2233    0.6131 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9867   -0.8080    1.6034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6197    0.8530    0.4835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5848    2.3501   -2.7430 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 15 18  1  0
 18 19  1  0
 19 20  2  0
 19 21  1  0
 13  9  1  0
 18 12  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  8 31  1  0
  9 32  1  0
 13 33  1  0
 16 34  1  0
 16 35  1  0
 16 36  1  0
 17 37  1  0
 17 38  1  0
 17 39  1  0
 18 40  1  0
 21 41  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

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

Chemical Formula

C₁₄H₂₀N₂O₄S

Average Molecular Weight

312.38

Monoisotopic Molecular Weight

312.114378306

IUPAC Name

6-(hex-3-enamido)-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

Traditional Name

6-(hex-3-enamido)-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

CCC=CCC(=O)NC1C2SC(C)(C)C(N2C1=O)C(O)=O

InChI Identifier

InChI=1S/C14H20N2O4S/c1-4-5-6-7-8(17)15-9-11(18)16-10(13(19)20)14(2,3)21-12(9)16/h5-6,9-10,12H,4,7H2,1-3H3,(H,15,17)(H,19,20)

InChI Key

QRLCJUNAKLMRGP-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-acyl-alpha amino acids and derivatives. N-acyl-alpha amino acids and derivatives are compounds containing an alpha amino acid (or a derivative thereof) which bears an acyl group at its terminal nitrogen atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

N-acyl-alpha amino acids and derivatives

Alternative Parents

Substituents

N-acyl-alpha amino acid or derivatives
Penam
Beta-lactam
Tertiary carboxylic acid amide
Thiazolidine
Azetidine
Carboxamide group
Lactam
Organoheterocyclic compound
Dialkylthioether
Organic 1,3-dipolar compound
Carboximidic acid
Carboximidic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Azacycle
Propargyl-type 1,3-dipolar organic compound
Hemithioaminal
Thioether
Organonitrogen compound
Organooxygen compound
Organic oxide
Hydrocarbon derivative
Carbonyl group
Organic nitrogen compound
Organic oxygen compound
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	2.12	ALOGPS
logP	0.92	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	3.62	ChemAxon
pKa (Strongest Basic)	-2	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	5	ChemAxon
Refractivity	79.35 m³·mol⁻¹	ChemAxon
Polarizability	32.24 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]+	177.898	30932474
DeepCCS	[M-H]-	175.54	30932474
DeepCCS	[M-2H]-	208.426	30932474
DeepCCS	[M+Na]+	183.991	30932474
AllCCS	[M+H]+	169.5	32859911
AllCCS	[M+H-H2O]+	166.7	32859911
AllCCS	[M+NH4]+	172.0	32859911
AllCCS	[M+Na]+	172.8	32859911
AllCCS	[M-H]-	173.2	32859911
AllCCS	[M+Na-2H]-	173.5	32859911
AllCCS	[M+HCOO]-	174.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Penicillin F	CCC=CCC(=O)NC1C2SC(C)(C)C(N2C1=O)C(O)=O	3582.4	Standard polar	33892256
Penicillin F	CCC=CCC(=O)NC1C2SC(C)(C)C(N2C1=O)C(O)=O	2140.7	Standard non polar	33892256
Penicillin F	CCC=CCC(=O)NC1C2SC(C)(C)C(N2C1=O)C(O)=O	2481.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Penicillin F,2TMS,isomer #1	CCC=CCC(=O)N(C1C(=O)N2C1SC(C)(C)C2C(=O)O[Si](C)(C)C)[Si](C)(C)C	2368.3	Semi standard non polar	33892256
Penicillin F,2TMS,isomer #1	CCC=CCC(=O)N(C1C(=O)N2C1SC(C)(C)C2C(=O)O[Si](C)(C)C)[Si](C)(C)C	2456.3	Standard non polar	33892256
Penicillin F,2TMS,isomer #1	CCC=CCC(=O)N(C1C(=O)N2C1SC(C)(C)C2C(=O)O[Si](C)(C)C)[Si](C)(C)C	2851.4	Standard polar	33892256
Penicillin F,2TBDMS,isomer #1	CCC=CCC(=O)N(C1C(=O)N2C1SC(C)(C)C2C(=O)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2805.5	Semi standard non polar	33892256
Penicillin F,2TBDMS,isomer #1	CCC=CCC(=O)N(C1C(=O)N2C1SC(C)(C)C2C(=O)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2892.3	Standard non polar	33892256
Penicillin F,2TBDMS,isomer #1	CCC=CCC(=O)N(C1C(=O)N2C1SC(C)(C)C2C(=O)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3019.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Penicillin F GC-MS (Non-derivatized) - 70eV, Positive	splash10-0v5c-9340000000-696ab4ad2c89786d1395	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Penicillin F GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Penicillin F GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Penicillin F GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Penicillin F GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Penicillin F 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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

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 F (HMDB0256230)

MOL for HMDB0256230 (Penicillin F)

3D MOL for HMDB0256230 (Penicillin F)

3D SDF for HMDB0256230 (Penicillin F)

3D-SDF for HMDB0256230 (Penicillin F)

PDB for HMDB0256230 (Penicillin F)

3D PDB for HMDB0256230 (Penicillin F)

SMILES for HMDB0256230 (Penicillin F)

INCHI for HMDB0256230 (Penicillin F)

Structure for HMDB0256230 (Penicillin F)

3D Structure for HMDB0256230 (Penicillin F)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra