MiMeDB: Showing metabocard for 6-aminopenicillanic acid (MMDBc0016197)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 06:52:54 UTC

Update Date

2024-10-17 16:08:22 UTC

Metabolite ID

MMDBc0016197

Metabolite Identification

Common Name

6-aminopenicillanic acid

Description

6-Aminopenicillanic acid, also known as 6-APA or penicin, 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. 6-Aminopenicillanic acid is a very strong basic compound (based on its pKa). 6-Aminopenicillanic acid exists in all living organisms, ranging from bacteria to humans.

Structure

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


  Mrv0541 06151311042D          

 14 15  0  0  1  0            999 V2000
    2.5600    0.7927    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
    2.5600    1.8968    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620    0.6773    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.6773    0.9323    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1477    0.9323    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7310    0.3489    0.0000 N   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
   -0.7310    2.3406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6773    1.7573    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620    2.0122    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7169    2.7968    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1649    3.4099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5239    2.9684    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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  5 10  1  6  0  0  0
 10 11  1  0  0  0  0
  2 11  1  0  0  0  0
 11 12  1  1  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0016197

> <DATABASE_NAME>
MIME

> <SMILES>
CC1(C)S[C@@H]2[C@H](N)C(=O)N2[C@H]1C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)/t3-,4+,6-/m1/s1

> <INCHI_KEY>
NGHVIOIJCVXTGV-ALEPSDHESA-N

> <FORMULA>
C8H12N2O3S

> <MOLECULAR_WEIGHT>
216.257

> <EXACT_MASS>
216.05686295

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
20.698966400238533

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

> <ALOGPS_LOGP>
-0.24

> <JCHEM_LOGP>
-2.8378366429456663

> <ALOGPS_LOGS>
-0.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.433548704443023

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.415152063079619

> <JCHEM_PKA_STRONGEST_BASIC>
7.403258608746982

> <JCHEM_POLAR_SURFACE_AREA>
83.63

> <JCHEM_REFRACTIVITY>
50.36210000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.55e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
penin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-JUN-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-JUN-13         0                                  
HETATM    1  C   UNK     0       4.779   1.480   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       4.779   3.541   0.000  0.00  0.00           C+0
HETATM    4  S   UNK     0       2.729   1.264   0.000  0.00  0.00           S+0
HETATM    5  C   UNK     0       1.264   1.740   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.276   1.740   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -1.365   0.651   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -0.276   3.280   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.365   4.369   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0       1.264   3.280   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       2.729   3.756   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.205   5.221   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.174   6.365   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       4.711   5.541   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4   11                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8    5   11                                                  
CONECT   11   10    2   12                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

Synonyms

Value	Source
(+)-6-Aminopenicillanic acid	ChEBI
(2S,5R,6R)-6-Amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid	ChEBI
6-Aminopenicillamine acid	ChEBI
6-Aminopenicillanate	ChEBI
6-APA	ChEBI
6-Aps	ChEBI
6beta-Aminopenicillanic acid	ChEBI
Aminopenicillanic acid	ChEBI
Penicin	ChEBI
Penin	ChEBI
Phenacyl 6-aminopenicillinate	ChEBI
(+)-6-Aminopenicillanate	Generator
(2S,5R,6R)-6-Amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate	Generator
6b-Aminopenicillanate	Generator
6b-Aminopenicillanic acid	Generator
6beta-Aminopenicillanate	Generator
6Β-aminopenicillanate	Generator
6Β-aminopenicillanic acid	Generator
Aminopenicillanate	Generator
Phenacyl 6-aminopenicillinic acid	Generator
6-APA CPD	HMDB
Aminopenicillanic acid, potassium salt	HMDB
Aminopenicillanic acid, sodium salt	HMDB

Molecular Formula

C₈H₁₂N₂O₃S

Average Mass

216.257

Monoisotopic Mass

216.05686295

IUPAC Name

(2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

Traditional Name

penin

CAS Registry Number

Not Available

SMILES

CC1(C)S[C@@H]2[C@H](N)C(=O)N2[C@H]1C(O)=O

InChI Identifier

InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)/t3-,4+,6-/m1/s1

InChI Key

NGHVIOIJCVXTGV-ALEPSDHESA-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
Alpha-amino acid or derivatives
Penam
Beta-lactam
Tertiary carboxylic acid amide
Thiazolidine
Amino acid or derivatives
Azetidine
Amino acid
Carboxamide group
Lactam
Carboxylic acid
Azacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Dialkylthioether
Hemithioaminal
Thioether
Amine
Primary aliphatic amine
Organic nitrogen compound
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Primary amine
Organopnictogen compound
Organic oxide
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

penicillanic acids (CHEBI:16705 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	55.5 g/L	ALOGPS
logP	-0.24	ALOGPS
logP	-2.8	ChemAxon
logS	-0.59	ALOGPS
pKa (Strongest Acidic)	3.42	ChemAxon
pKa (Strongest Basic)	7.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	83.63 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	50.36 m³·mol⁻¹	ChemAxon
Polarizability	20.7 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0uxr-1930000000-8b3dad9f5db3d8512110	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0uxr-1930000000-14be07ea22813265cdf3	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0uxr-1930000000-8b3dad9f5db3d8512110	2018-05-18	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0uxr-1930000000-14be07ea22813265cdf3	2018-05-18	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4i-9200000000-e33fe5dc6f7515fb41d5	2017-09-20	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-05fr-9220000000-0d97e3938474120b9e87	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-00di-9300000000-e9bd620d9e681c167ae5	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-00di-9300000000-d0d73fa955283a4de8e1	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-00dr-0900000000-c0222f314effc3d7ad8a	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-00dr-0900000000-f17a9cc1b1e04e3b7e71	2017-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-9330000000-0853f16f9d9fb3a3f86e	2016-06-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-1910000000-fbdab9a3772fcfd7c0c8	2016-06-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9200000000-6b276429012b5ee9844f	2016-06-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-9200000000-9ffda48df6b90d12f303	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0ab9-9200000000-f630fdfcda8c288572e2	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00di-9200000000-e7d207177892f580f3c9	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00kr-0950000000-bbef363560f5d2d25c16	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-1910000000-8a0d3e001608783c72a0	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-014i-9800000000-64b11c9f70ce0cb2d2b0	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-9100000000-25f442a83faa3f7da843	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00di-9200000000-7d7718220a18a63d2655	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00di-9000000000-766302f54e49d015548c	2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Kidney
Liver

Tissue Locations

Kidney
Liver

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Kidney	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Liver	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597

External Links

HMDB ID

HMDB0060618

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

C02954

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

6-APA

METLIN ID

Not Available

PubChem Compound

11082

PDB ID

Not Available

ChEBI ID

16705

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Shimizu T, Souma S, Nagakura N, Masuzawa T, Iwamoto Y, Yanagihara Y: Epitope analysis of aztreonam by antiaztreonam monoclonal antibodies and possible consequences in beta-lactams hypersensitivity. Int Arch Allergy Immunol. 1992;98(4):392-7. doi: 10.1159/000236216. [PubMed:1384868 ]
Harle DG, Baldo BA: Identification of penicillin allergenic determinants that bind IgE antibodies in the sera of subjects with penicillin allergy. Mol Immunol. 1990 Nov;27(11):1063-71. doi: 10.1016/0161-5890(90)90094-g. [PubMed:1701026 ]
Zhao Y, Qiao H: Detection of specific IgE antibodies to major and minor antigenic determinants in sera of penicillin allergic patients. Chin Med J (Engl). 2003 Dec;116(12):1904-10. [PubMed:14687482 ]
Ariza A, Barrionuevo E, Mayorga C, Montanez MI, Perez-Inestrosa E, Ruiz-Sanchez A, Rodriguez-Gueant RM, Fernandez TD, Gueant JL, Torres MJ, Blanca M: IgE to penicillins with different specificities can be identified by a multiepitope macromolecule: Bihaptenic penicillin structures and IgE specificities. J Immunol Methods. 2014 Apr;406:43-50. doi: 10.1016/j.jim.2014.03.001. Epub 2014 Mar 13. [PubMed:24631718 ]

Showing metabocard for 6-aminopenicillanic acid (MMDBc0016197)

MOL for #<Metabolite:0x0000562ee4d3bf58>

3D MOL for #<Metabolite:0x0000562ee4d3bf58>

3D SDF for #<Metabolite:0x0000562ee4d3bf58>

3D-SDF for #<Metabolite:0x0000562ee4d3bf58>

PDB for #<Metabolite:0x0000562ee4d3bf58>

3D PDB for #<Metabolite:0x0000562ee4d3bf58>

SMILES for #<Metabolite:0x0000562ee4d3bf58>

INCHI for #<Metabolite:0x0000562ee4d3bf58>

Structure for #<Metabolite:0x0000562ee4d3bf58>

3D Structure for #<Metabolite:0x0000562ee4d3bf58>