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Showing metabocard for Penicillanic acid (HMDB0256227)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 16:33:12 UTC
Update Date2021-09-26 23:11:44 UTC
HMDB IDHMDB0256227
Secondary Accession NumbersNone
Metabolite Identification
Common NamePenicillanic acid
DescriptionPenicillanic acid, also known as penicillanate, 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 a significant number of articles have been published on Penicillanic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). Penicillanic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Penicillanic 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0256227 (Penicillanic acid)

  Mrv1652309112118332D          

 13 14  0  0  0  0            999 V2000
    2.5600    1.8968    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9469    1.3448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620    0.6773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6773    0.9323    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6773    1.7573    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620    2.0122    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1477    1.7573    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
   -0.7310    0.3489    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7169   -0.1073    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1649   -0.7204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5239   -0.2788    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5600    0.7927    0.0000 C   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
  2  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  2  0  0  0  0
  3 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  2 13  1  0  0  0  0
M  END
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3D MOL for HMDB0256227 (Penicillanic acid)

HMDB0256227
     RDKit          3D
Penicillanic acid
 24 25  0  0  0  0  0  0  0  0999 V2000
   -1.3655   -0.9729    1.2988 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9272   -0.7810   -0.1149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9816   -1.1129   -1.1328 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5219   -1.8399   -0.5137 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.6964   -0.4654   -0.8476 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8889   -0.4304    0.0706 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2831    0.8648    0.5074 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8189    1.8163    1.1648 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0322    0.5650   -0.0709 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3676    0.5940   -0.3852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0678    1.6583    0.3294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3050    1.8282    0.1718 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4295    2.5344    1.2110 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1318   -0.2385    1.5351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4985   -0.7813    1.9545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7352   -2.0044    1.4079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4605   -1.1164   -2.1352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4253   -2.0980   -0.9602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7019   -0.2801   -1.1824 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8646   -0.2573   -1.8994 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8514   -1.2344    0.8033 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8189   -0.3205   -0.5170 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4419    0.7454   -1.4994 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0632    3.3267    0.8040 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  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 10  2  1  0
  9  5  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  3 17  1  0
  3 18  1  0
  3 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
 10 23  1  0
 13 24  1  0
M  END
Download

3D SDF for HMDB0256227 (Penicillanic acid)

  Mrv1652309112118332D          

 13 14  0  0  0  0            999 V2000
    2.5600    1.8968    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9469    1.3448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620    0.6773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6773    0.9323    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6773    1.7573    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620    2.0122    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1477    1.7573    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
   -0.7310    0.3489    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7169   -0.1073    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1649   -0.7204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5239   -0.2788    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5600    0.7927    0.0000 C   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
  2  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  2  0  0  0  0
  3 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  2 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256227

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1(C)SC2CC(=O)N2C1C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H11NO3S/c1-8(2)6(7(11)12)9-4(10)3-5(9)13-8/h5-6H,3H2,1-2H3,(H,11,12)

> <INCHI_KEY>
RBKMMJSQKNKNEV-UHFFFAOYSA-N

> <FORMULA>
C8H11NO3S

> <MOLECULAR_WEIGHT>
201.24

> <EXACT_MASS>
201.045964392

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
19.334403883401002

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
0.32

> <JCHEM_LOGP>
0.24953178766666628

> <ALOGPS_LOGS>
-0.79

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6902060003388937

> <JCHEM_PKA_STRONGEST_BASIC>
-3.190485812412524

> <JCHEM_POLAR_SURFACE_AREA>
57.61

> <JCHEM_REFRACTIVITY>
47.36640000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.26e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
penicillanic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0256227 (Penicillanic acid)

HMDB0256227
     RDKit          3D
Penicillanic acid
 24 25  0  0  0  0  0  0  0  0999 V2000
   -1.3655   -0.9729    1.2988 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9272   -0.7810   -0.1149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9816   -1.1129   -1.1328 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5219   -1.8399   -0.5137 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.6964   -0.4654   -0.8476 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8889   -0.4304    0.0706 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2831    0.8648    0.5074 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8189    1.8163    1.1648 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0322    0.5650   -0.0709 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3676    0.5940   -0.3852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0678    1.6583    0.3294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3050    1.8282    0.1718 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4295    2.5344    1.2110 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1318   -0.2385    1.5351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4985   -0.7813    1.9545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7352   -2.0044    1.4079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4605   -1.1164   -2.1352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4253   -2.0980   -0.9602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7019   -0.2801   -1.1824 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8646   -0.2573   -1.8994 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8514   -1.2344    0.8033 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8189   -0.3205   -0.5170 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4419    0.7454   -1.4994 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0632    3.3267    0.8040 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  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 10  2  1  0
  9  5  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  3 17  1  0
  3 18  1  0
  3 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
 10 23  1  0
 13 24  1  0
M  END
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PDB for HMDB0256227 (Penicillanic acid)

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       4.779   3.541   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.634   2.510   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.729   1.264   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       1.264   1.740   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.264   3.280   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0       2.729   3.756   0.000  0.00  0.00           S+0
HETATM    7  C   UNK     0      -0.276   3.280   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.276   1.740   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.365   0.651   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       3.205  -0.200   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.174  -1.345   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       4.711  -0.520   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.779   1.480   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    6   13                                             
CONECT    3    2    4   10                                                  
CONECT    4    3    5    8                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    2                                                       
CONECT    7    5    8                                                       
CONECT    8    7    4    9                                                  
CONECT    9    8                                                            
CONECT   10    3   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    2                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END
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3D PDB for HMDB0256227 (Penicillanic acid)

COMPND    HMDB0256227
HETATM    1  C1  UNL     1      -1.366  -0.973   1.299  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.927  -0.781  -0.115  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.982  -1.113  -1.133  1.00  0.00           C  
HETATM    4  S1  UNL     1       0.522  -1.840  -0.514  1.00  0.00           S  
HETATM    5  C4  UNL     1       1.696  -0.465  -0.848  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.889  -0.430   0.071  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.283   0.865   0.507  1.00  0.00           C  
HETATM    8  O1  UNL     1       2.819   1.816   1.165  1.00  0.00           O  
HETATM    9  N1  UNL     1       1.032   0.565  -0.071  1.00  0.00           N  
HETATM   10  C7  UNL     1      -0.368   0.594  -0.385  1.00  0.00           C  
HETATM   11  C8  UNL     1      -1.068   1.658   0.329  1.00  0.00           C  
HETATM   12  O2  UNL     1      -2.305   1.828   0.172  1.00  0.00           O  
HETATM   13  O3  UNL     1      -0.429   2.534   1.211  1.00  0.00           O  
HETATM   14  H1  UNL     1      -2.132  -0.238   1.535  1.00  0.00           H  
HETATM   15  H2  UNL     1      -0.499  -0.781   1.955  1.00  0.00           H  
HETATM   16  H3  UNL     1      -1.735  -2.004   1.408  1.00  0.00           H  
HETATM   17  H4  UNL     1      -1.461  -1.116  -2.135  1.00  0.00           H  
HETATM   18  H5  UNL     1      -2.425  -2.098  -0.960  1.00  0.00           H  
HETATM   19  H6  UNL     1      -2.702  -0.280  -1.182  1.00  0.00           H  
HETATM   20  H7  UNL     1       1.865  -0.257  -1.899  1.00  0.00           H  
HETATM   21  H8  UNL     1       2.851  -1.234   0.803  1.00  0.00           H  
HETATM   22  H9  UNL     1       3.819  -0.320  -0.517  1.00  0.00           H  
HETATM   23  H10 UNL     1      -0.442   0.745  -1.499  1.00  0.00           H  
HETATM   24  H11 UNL     1       0.063   3.327   0.804  1.00  0.00           H  
CONECT    1    2   14   15   16
CONECT    2    3    4   10
CONECT    3   17   18   19
CONECT    4    5
CONECT    5    6    9   20
CONECT    6    7   21   22
CONECT    7    8    8    9
CONECT    9   10
CONECT   10   11   23
CONECT   11   12   12   13
CONECT   13   24
END
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SMILES for HMDB0256227 (Penicillanic acid)

CC1(C)SC2CC(=O)N2C1C(O)=O
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INCHI for HMDB0256227 (Penicillanic acid)

InChI=1S/C8H11NO3S/c1-8(2)6(7(11)12)9-4(10)3-5(9)13-8/h5-6H,3H2,1-2H3,(H,11,12)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
PenicillanateGenerator
3,3-Dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylateHMDB
Chemical FormulaC8H11NO3S
Average Molecular Weight201.24
Monoisotopic Molecular Weight201.045964392
IUPAC Name3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
Traditional Namepenicillanic acid
CAS Registry NumberNot Available
SMILES
CC1(C)SC2CC(=O)N2C1C(O)=O
InChI Identifier
InChI=1S/C8H11NO3S/c1-8(2)6(7(11)12)9-4(10)3-5(9)13-8/h5-6H,3H2,1-2H3,(H,11,12)
InChI KeyRBKMMJSQKNKNEV-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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids and derivatives
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
  • Penam
  • Beta-lactam
  • Tertiary carboxylic acid amide
  • Thiazolidine
  • Azetidine
  • Carboxamide group
  • Lactam
  • Thioether
  • Azacycle
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Hemithioaminal
  • Dialkylthioether
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID10667824
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound12314047
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]