Hmdb loader
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 11:12:24 UTC
Update Date2021-09-26 23:06:01 UTC
HMDB IDHMDB0253036
Secondary Accession NumbersNone
Metabolite Identification
Common NameHadacidin
DescriptionHadacidin, also known as hadicidine, belongs to the class of organic compounds known as n-formyl-alpha amino acids. N-formyl-alpha amino acids are compounds containing an alpha amino acid which bears a formyl group at its terminal nitrogen atom. Hadacidin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Hadacidin. This compound has been identified in human blood as reported by (PMID: 31557052 ). Hadacidin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Hadacidin 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
Thumb
Synonyms
ValueSource
[Formyl(hydroxy)amino]acetic acidChEBI
N-Formyl hydroxyaminoacetic acidChEBI
N-Formyl-N- hydroxyaminoacetic acidChEBI
N-Hydroxyformamidoacetic acidChEBI
[Formyl(hydroxy)amino]acetateGenerator
N-Formyl hydroxyaminoacetateGenerator
N-Formyl-N- hydroxyaminoacetateGenerator
N-HydroxyformamidoacetateGenerator
N-Formyl-N-hydroxyglycineMeSH
Hadacidin, monosodium saltMeSH
HadicidineMeSH
Chemical FormulaC3H5NO4
Average Molecular Weight119.0761
Monoisotopic Molecular Weight119.021857653
IUPAC Name2-(N-hydroxyformamido)acetic acid
Traditional Namehadacidin
CAS Registry NumberNot Available
SMILES
ON(CC(O)=O)C=O
InChI Identifier
InChI=1S/C3H5NO4/c5-2-4(8)1-3(6)7/h2,8H,1H2,(H,6,7)
InChI KeyURJHVPKUWOUENU-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as n-formyl-alpha amino acids. N-formyl-alpha amino acids are compounds containing an alpha amino acid which bears a formyl group at its terminal nitrogen atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentN-formyl-alpha amino acids
Alternative Parents
Substituents
  • N-formyl-alpha-amino acid
  • N-hydroxyl-alpha-amino acid
  • Hydroxamic acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
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
PropertyValueSource
logP-0.97ALOGPS
logP-1.4ChemAxon
logS-0.38ALOGPS
pKa (Strongest Acidic)3.28ChemAxon
pKa (Strongest Basic)-5.9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area77.84 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity22.72 m³·mol⁻¹ChemAxon
Polarizability9.37 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+119.90430932474
DeepCCS[M-H]-117.74730932474
DeepCCS[M-2H]-153.92130932474
DeepCCS[M+Na]+128.49930932474
AllCCS[M+H]+128.032859911
AllCCS[M+H-H2O]+123.832859911
AllCCS[M+NH4]+131.932859911
AllCCS[M+Na]+133.032859911
AllCCS[M-H]-120.232859911
AllCCS[M+Na-2H]-123.432859911
AllCCS[M+HCOO]-127.032859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20229.3582 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.3 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid759.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid354.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid79.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid238.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid69.2 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid264.8 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid305.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)328.9 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid616.1 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid130.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid901.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid226.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid271.9 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate706.5 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA267.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water320.6 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
HadacidinON(CC(O)=O)C=O1890.8Standard polar33892256
HadacidinON(CC(O)=O)C=O1265.0Standard non polar33892256
HadacidinON(CC(O)=O)C=O1245.2Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Hadacidin GC-MS (Non-derivatized) - 70eV, Positivesplash10-054o-9000000000-f95c6a45516248cdb55e2017-08-28Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hadacidin GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hadacidin GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hadacidin GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hadacidin 10V, Positive-QTOFsplash10-00di-1900000000-2ff284e07d919fd83ee12017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hadacidin 20V, Positive-QTOFsplash10-00di-2900000000-106b659006e7de5068002017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hadacidin 40V, Positive-QTOFsplash10-006x-9000000000-162e5cdb332337bfd8852017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hadacidin 10V, Negative-QTOFsplash10-014i-0900000000-8de46ef0ccbe3eae41432017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hadacidin 20V, Negative-QTOFsplash10-06di-9700000000-afddf8769d6571d3b3872017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hadacidin 40V, Negative-QTOFsplash10-0pb9-9300000000-c731cadc6a6af241915d2017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hadacidin 10V, Positive-QTOFsplash10-00dl-9300000000-acbcf35b054048a0fa292021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hadacidin 20V, Positive-QTOFsplash10-00dj-9000000000-6e796d5b65526b1ab9602021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hadacidin 40V, Positive-QTOFsplash10-00di-9000000000-6affeabe5db7cc9bb98b2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hadacidin 10V, Negative-QTOFsplash10-0006-9000000000-6e393bd75e75623033f02021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hadacidin 20V, Negative-QTOFsplash10-00dl-9000000000-5bba9fb9de82b24f70122021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hadacidin 40V, Negative-QTOFsplash10-00dl-9000000000-3481801e9e5ef5fcacc82021-10-12Wishart LabView Spectrum
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 IDDB02109
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID12194
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkHadacidin
METLIN IDNot Available
PubChem Compound12717
PDB IDNot Available
ChEBI ID43040
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 ]