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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-06-15 18:06:03 UTC
Update Date2021-09-14 15:46:00 UTC
HMDB IDHMDB0060618
Secondary Accession Numbers
  • HMDB60618
Metabolite Identification
Common Name6-Aminopenicillanic acid
Description6-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
Data?1563866083
Synonyms
ValueSource
(+)-6-Aminopenicillanic acidChEBI
(2S,5R,6R)-6-Amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acidChEBI
6-Aminopenicillamine acidChEBI
6-AminopenicillanateChEBI
6-APAChEBI
6-ApsChEBI
6beta-Aminopenicillanic acidChEBI
Aminopenicillanic acidChEBI
PenicinChEBI
PeninChEBI
Phenacyl 6-aminopenicillinateChEBI
(+)-6-AminopenicillanateGenerator
(2S,5R,6R)-6-Amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylateGenerator
6b-AminopenicillanateGenerator
6b-Aminopenicillanic acidGenerator
6beta-AminopenicillanateGenerator
6Β-aminopenicillanateGenerator
6Β-aminopenicillanic acidGenerator
AminopenicillanateGenerator
Phenacyl 6-aminopenicillinic acidGenerator
6-APA CPDHMDB
Aminopenicillanic acid, potassium saltHMDB
Aminopenicillanic acid, sodium saltHMDB
Chemical FormulaC8H12N2O3S
Average Molecular Weight216.257
Monoisotopic Molecular Weight216.05686295
IUPAC Name(2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
Traditional Namepenin
CAS Registry NumberNot 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 KeyNGHVIOIJCVXTGV-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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentDipeptides
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 FrameworkAliphatic heteropolycyclic compounds
External Descriptors
Ontology
Disposition

Biological location

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
PropertyValueSource
Water Solubility55.5 g/LALOGPS
logP-0.24ALOGPS
logP-2.8ChemAxon
logS-0.59ALOGPS
pKa (Strongest Acidic)3.42ChemAxon
pKa (Strongest Basic)7.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area83.63 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity50.36 m³·mol⁻¹ChemAxon
Polarizability20.7 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+148.65231661259
DarkChem[M-H]-142.94131661259
DeepCCS[M+H]+156.26930932474
DeepCCS[M-H]-153.88230932474
DeepCCS[M-2H]-186.78730932474
DeepCCS[M+Na]+162.33330932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
6-Aminopenicillanic acidCC1(C)S[C@@H]2[C@H](N)C(=O)N2[C@H]1C(O)=O2850.7Standard polar33892256
6-Aminopenicillanic acidCC1(C)S[C@@H]2[C@H](N)C(=O)N2[C@H]1C(O)=O1861.4Standard non polar33892256
6-Aminopenicillanic acidCC1(C)S[C@@H]2[C@H](N)C(=O)N2[C@H]1C(O)=O1860.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
6-Aminopenicillanic acid,1TMS,isomer #1CC1(C)S[C@@H]2[C@H](N)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C1850.4Semi standard non polar33892256
6-Aminopenicillanic acid,1TMS,isomer #2CC1(C)S[C@@H]2[C@H](N[Si](C)(C)C)C(=O)N2[C@H]1C(=O)O1897.3Semi standard non polar33892256
6-Aminopenicillanic acid,2TMS,isomer #1CC1(C)S[C@@H]2[C@H](N[Si](C)(C)C)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C1937.4Semi standard non polar33892256
6-Aminopenicillanic acid,2TMS,isomer #1CC1(C)S[C@@H]2[C@H](N[Si](C)(C)C)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C1942.7Standard non polar33892256
6-Aminopenicillanic acid,2TMS,isomer #1CC1(C)S[C@@H]2[C@H](N[Si](C)(C)C)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C2490.7Standard polar33892256
6-Aminopenicillanic acid,2TMS,isomer #2CC1(C)S[C@@H]2[C@H](N([Si](C)(C)C)[Si](C)(C)C)C(=O)N2[C@H]1C(=O)O1944.0Semi standard non polar33892256
6-Aminopenicillanic acid,2TMS,isomer #2CC1(C)S[C@@H]2[C@H](N([Si](C)(C)C)[Si](C)(C)C)C(=O)N2[C@H]1C(=O)O2042.0Standard non polar33892256
6-Aminopenicillanic acid,2TMS,isomer #2CC1(C)S[C@@H]2[C@H](N([Si](C)(C)C)[Si](C)(C)C)C(=O)N2[C@H]1C(=O)O2479.8Standard polar33892256
6-Aminopenicillanic acid,3TMS,isomer #1CC1(C)S[C@@H]2[C@H](N([Si](C)(C)C)[Si](C)(C)C)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C1997.7Semi standard non polar33892256
6-Aminopenicillanic acid,3TMS,isomer #1CC1(C)S[C@@H]2[C@H](N([Si](C)(C)C)[Si](C)(C)C)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C2116.9Standard non polar33892256
6-Aminopenicillanic acid,3TMS,isomer #1CC1(C)S[C@@H]2[C@H](N([Si](C)(C)C)[Si](C)(C)C)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C2213.6Standard polar33892256
6-Aminopenicillanic acid,1TBDMS,isomer #1CC1(C)S[C@@H]2[C@H](N)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C(C)(C)C2077.2Semi standard non polar33892256
6-Aminopenicillanic acid,1TBDMS,isomer #2CC1(C)S[C@@H]2[C@H](N[Si](C)(C)C(C)(C)C)C(=O)N2[C@H]1C(=O)O2110.2Semi standard non polar33892256
6-Aminopenicillanic acid,2TBDMS,isomer #1CC1(C)S[C@@H]2[C@H](N[Si](C)(C)C(C)(C)C)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C(C)(C)C2346.3Semi standard non polar33892256
6-Aminopenicillanic acid,2TBDMS,isomer #1CC1(C)S[C@@H]2[C@H](N[Si](C)(C)C(C)(C)C)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C(C)(C)C2458.8Standard non polar33892256
6-Aminopenicillanic acid,2TBDMS,isomer #1CC1(C)S[C@@H]2[C@H](N[Si](C)(C)C(C)(C)C)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C(C)(C)C2626.3Standard polar33892256
6-Aminopenicillanic acid,2TBDMS,isomer #2CC1(C)S[C@@H]2[C@H](N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)N2[C@H]1C(=O)O2400.5Semi standard non polar33892256
6-Aminopenicillanic acid,2TBDMS,isomer #2CC1(C)S[C@@H]2[C@H](N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)N2[C@H]1C(=O)O2525.3Standard non polar33892256
6-Aminopenicillanic acid,2TBDMS,isomer #2CC1(C)S[C@@H]2[C@H](N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)N2[C@H]1C(=O)O2615.6Standard polar33892256
6-Aminopenicillanic acid,3TBDMS,isomer #1CC1(C)S[C@@H]2[C@H](N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C(C)(C)C2626.8Semi standard non polar33892256
6-Aminopenicillanic acid,3TBDMS,isomer #1CC1(C)S[C@@H]2[C@H](N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C(C)(C)C2799.0Standard non polar33892256
6-Aminopenicillanic acid,3TBDMS,isomer #1CC1(C)S[C@@H]2[C@H](N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C(C)(C)C2532.1Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - 6-Aminopenicillanic acid GC-EI-TOF (Non-derivatized)splash10-0uxr-1930000000-8b3dad9f5db3d85121102017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - 6-Aminopenicillanic acid GC-EI-TOF (Non-derivatized)splash10-0uxr-1930000000-14be07ea22813265cdf32017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - 6-Aminopenicillanic acid GC-EI-TOF (Non-derivatized)splash10-0uxr-1930000000-8b3dad9f5db3d85121102018-05-18HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - 6-Aminopenicillanic acid GC-EI-TOF (Non-derivatized)splash10-0uxr-1930000000-14be07ea22813265cdf32018-05-18HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 6-Aminopenicillanic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4i-9200000000-e33fe5dc6f7515fb41d52017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 6-Aminopenicillanic acid GC-MS (1 TMS) - 70eV, Positivesplash10-05fr-9220000000-0d97e3938474120b9e872017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 6-Aminopenicillanic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - 6-Aminopenicillanic acid Linear Ion Trap , negative-QTOFsplash10-00di-9300000000-e9bd620d9e681c167ae52017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 6-Aminopenicillanic acid Linear Ion Trap , negative-QTOFsplash10-00di-9300000000-d0d73fa955283a4de8e12017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 6-Aminopenicillanic acid Linear Ion Trap , positive-QTOFsplash10-00dr-0900000000-c0222f314effc3d7ad8a2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 6-Aminopenicillanic acid Linear Ion Trap , positive-QTOFsplash10-00dr-0900000000-f17a9cc1b1e04e3b7e712017-09-14HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Aminopenicillanic acid 10V, Positive-QTOFsplash10-0a4i-9330000000-0853f16f9d9fb3a3f86e2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Aminopenicillanic acid 20V, Positive-QTOFsplash10-03di-1910000000-fbdab9a3772fcfd7c0c82016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Aminopenicillanic acid 40V, Positive-QTOFsplash10-0a4i-9200000000-6b276429012b5ee9844f2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Aminopenicillanic acid 10V, Negative-QTOFsplash10-00di-9200000000-9ffda48df6b90d12f3032016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Aminopenicillanic acid 20V, Negative-QTOFsplash10-0ab9-9200000000-f630fdfcda8c288572e22016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Aminopenicillanic acid 40V, Negative-QTOFsplash10-00di-9200000000-e7d207177892f580f3c92016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Aminopenicillanic acid 10V, Positive-QTOFsplash10-00kr-0950000000-bbef363560f5d2d25c162021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Aminopenicillanic acid 20V, Positive-QTOFsplash10-03di-1910000000-8a0d3e001608783c72a02021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Aminopenicillanic acid 40V, Positive-QTOFsplash10-014i-9800000000-64b11c9f70ce0cb2d2b02021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Aminopenicillanic acid 10V, Negative-QTOFsplash10-00di-9100000000-25f442a83faa3f7da8432021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Aminopenicillanic acid 20V, Negative-QTOFsplash10-00di-9200000000-7d7718220a18a63d26552021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Aminopenicillanic acid 40V, Negative-QTOFsplash10-00di-9000000000-766302f54e49d015548c2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Kidney
  • Liver
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
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 IDNot Available
KEGG Compound IDC02954
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link6-APA
METLIN IDNot Available
PubChem Compound11082
PDB IDNot Available
ChEBI ID16705
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. 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. [PubMed:1384868 ]
  2. 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 ]
  3. 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. [PubMed:1701026 ]
  4. 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 ]