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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 06:16:39 UTC
Update Date2021-09-24 06:16:40 UTC
HMDB IDHMDB0303995
Secondary Accession NumbersNone
Metabolite Identification
Common Name(S)-2,3-dihydrodipicolinate
Description(s)-2,3-dihydrodipicolinate, also known as (S)-2,3-dihydropyridine-2,6-dicarboxylate or 2,3-di-H-dipicolinic acid, belongs to alpha amino acids and derivatives class of compounds. Those 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 (s)-2,3-dihydrodipicolinate is slightly soluble (in water) and a weakly acidic compound (based on its pKa). (s)-2,3-dihydrodipicolinate can be found in a number of food items such as american cranberry, moth bean, parsnip, and giant butterbur, which makes (s)-2,3-dihydrodipicolinate a potential biomarker for the consumption of these food products.
Structure
Thumb
Synonyms
ValueSource
(S)-2,3-DihydrodipicolinateChEBI
(S)-2,3-Dihydropyridine-2,6-dicarboxylateChEBI
L-2,3-DihydrodipicolinateChEBI
(S)-2,3-Dihydrodipicolinic acidGenerator
(S)-2,3-Dihydropyridine-2,6-dicarboxylic acidGenerator
L-2,3-Dihydrodipicolinic acidGenerator
(S)-2,3-Dihydrodipicolinic acid(2-)Generator
Chemical FormulaC7H5NO4
Average Molecular Weight167.121
Monoisotopic Molecular Weight167.022954805
IUPAC Name(2S)-2,3-dihydropyridine-2,6-dicarboxylate
Traditional NameL-2,3-dihydrodipicolinate
CAS Registry NumberNot Available
SMILES
[H][C@]1(CC=CC(=N1)C([O-])=O)C([O-])=O
InChI Identifier
InChI=1S/C7H7NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h1-2,5H,3H2,(H,9,10)(H,11,12)/p-2/t5-/m0/s1
InChI KeyUWOCFOFVIBZJGH-YFKPBYRVSA-L
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
  • Dihydropyridinecarboxylic acid derivative
  • Dihydropyridine
  • Dicarboxylic acid or derivatives
  • Hydropyridine
  • Ketimine
  • Carboxylic acid
  • Azacycle
  • Organoheterocyclic compound
  • Organic nitrogen compound
  • Carbonyl group
  • Organonitrogen compound
  • Organooxygen compound
  • Imine
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic anion
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
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
logP0.1ALOGPS
logP0.66ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)3.17ChemAxon
pKa (Strongest Basic)-1.1ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area92.62 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity61.04 m³·mol⁻¹ChemAxon
Polarizability14.16 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+135.8232859911
AllCCS[M+H-H2O]+131.35632859911
AllCCS[M+Na]+141.18332859911
AllCCS[M+NH4]+139.98232859911
AllCCS[M-H]-125.61232859911
AllCCS[M+Na-2H]-126.39432859911
AllCCS[M+HCOO]-127.3232859911
DeepCCS[M+H]+131.12730932474
DeepCCS[M-H]-128.72830932474
DeepCCS[M-2H]-163.83730932474
DeepCCS[M+Na]+138.97830932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202211.8062 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20224.77 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1488.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid378.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid119.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid268.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid103.4 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid384.4 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 Acid406.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)183.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid907.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid347.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1148.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid254.9 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid323.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate712.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA267.7 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water167.2 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030155
KNApSAcK IDNot Available
Chemspider ID4573840
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5460228
PDB IDNot Available
ChEBI ID30620
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 ReferencesNot Available