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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2006-08-12 22:40:07 UTC
Update Date2021-09-14 15:46:28 UTC
HMDB IDHMDB0003518
Secondary Accession Numbers
  • HMDB03518
Metabolite Identification
Common NameHomocitric acid
DescriptionHomocitric acid (CAS: 3562-74-1) is a normal urinary organic acid (PMID: 14708889 ). Homocitric acid is a citric acid analogue found as a minor metabolite in urine samples from patients with propionic acidaemia. Homocitric acid is formed by citrate synthase due to propionyl-CoA carboxylase deficiency (by the citrate synthase condensation reaction of alpha-ketoglutarate with acetyl coenzyme A and propionyl coenzyme A) (PMID: 7850997 ). Homocitric acid has been identified in the human placenta (PMID: 32033212 ).
Structure
Data?1582752279
Synonyms
ValueSource
(R)-2-Hydroxy-1,2,4-butanetricarboxylic acidChEBI
(R)-2-Hydroxybutane-1,2,4-tricarboxylic acidChEBI
(R)-Homocitric acidChEBI
3-Hydroxy-3-carboxyadipic acidChEBI
HomocitrateChEBI
(R)-2-Hydroxy-1,2,4-butanetricarboxylateGenerator
(R)-2-Hydroxybutane-1,2,4-tricarboxylateGenerator
(R)-HomocitrateGenerator
3-Hydroxy-3-carboxyadipateGenerator
2-Hydroxybutane-1,2,4-tricarboxylateHMDB
(2R)-2-Hydroxy-1,2,4-butanetricarboxylateHMDB
(2R)-2-Hydroxy-1,2,4-butanetricarboxylic acidHMDB
(±)-homocitrateHMDB
(±)-homocitric acidHMDB
2-Hydroxy-1,2,4-butanetricarboxylateHMDB
2-Hydroxy-1,2,4-butanetricarboxylic acidHMDB
Homocitric acidHMDB
Chemical FormulaC7H10O7
Average Molecular Weight206.1501
Monoisotopic Molecular Weight206.042652674
IUPAC Name(2R)-2-hydroxybutane-1,2,4-tricarboxylic acid
Traditional Name(R)-homocitric acid
CAS Registry Number13052-73-8
SMILES
OC(=O)CC[C@@](O)(CC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C7H10O7/c8-4(9)1-2-7(14,6(12)13)3-5(10)11/h14H,1-3H2,(H,8,9)(H,10,11)(H,12,13)/t7-/m1/s1
InChI KeyXKJVEVRQMLKSMO-SSDOTTSWSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassTricarboxylic acids and derivatives
Direct ParentTricarboxylic acids and derivatives
Alternative Parents
Substituents
  • Tricarboxylic acid or derivatives
  • Hydroxy acid
  • Alpha-hydroxy acid
  • Tertiary alcohol
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Disposition

Biological location

Source

Route of exposure

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Spectral Properties

Experimental Collision Cross Sections

PredictorAdduct TypeData SourceCCS Value (Å2)Reference
AllCCS[M-H]-Not Available129.995http://allccs.zhulab.cn/database/detail?ID=AllCCS00000061
Predicted Molecular Properties
PropertyValueSource
Water Solubility191 g/LALOGPS
logP10(-1.5) g/LALOGPS
logP10(-1) g/LChemAxon
logS10(-0.03) g/LALOGPS
pKa (Strongest Acidic)3.09ChemAxon
pKa (Strongest Basic)-4.1ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area132.13 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity40.38 m³·mol⁻¹ChemAxon
Polarizability17.44 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Spectral Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+145.71531661259
DarkChem[M-H]-137.88631661259

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Homocitric acid,1TMS,#1C[Si](C)(C)OC(=O)CC[C@@](O)(CC(=O)O)C(=O)O1780.4Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,1TMS,#2C[Si](C)(C)O[C@](CCC(=O)O)(CC(=O)O)C(=O)O1831.0Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,1TMS,#3C[Si](C)(C)OC(=O)C[C@](O)(CCC(=O)O)C(=O)O1781.9Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,1TMS,#4C[Si](C)(C)OC(=O)[C@@](O)(CCC(=O)O)CC(=O)O1728.1Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,2TMS,#1C[Si](C)(C)OC(=O)CC[C@](CC(=O)O)(O[Si](C)(C)C)C(=O)O1860.2Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,2TMS,#2C[Si](C)(C)OC(=O)CC[C@@](O)(CC(=O)O[Si](C)(C)C)C(=O)O1855.8Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,2TMS,#3C[Si](C)(C)OC(=O)CC[C@@](O)(CC(=O)O)C(=O)O[Si](C)(C)C1805.3Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,2TMS,#4C[Si](C)(C)OC(=O)C[C@@](CCC(=O)O)(O[Si](C)(C)C)C(=O)O1853.3Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,2TMS,#5C[Si](C)(C)OC(=O)[C@@](CCC(=O)O)(CC(=O)O)O[Si](C)(C)C1836.1Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,2TMS,#6C[Si](C)(C)OC(=O)C[C@](O)(CCC(=O)O)C(=O)O[Si](C)(C)C1814.2Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,3TMS,#1C[Si](C)(C)OC(=O)CC[C@](CC(=O)O[Si](C)(C)C)(O[Si](C)(C)C)C(=O)O1865.3Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,3TMS,#2C[Si](C)(C)OC(=O)CC[C@](CC(=O)O)(O[Si](C)(C)C)C(=O)O[Si](C)(C)C1884.8Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,3TMS,#3C[Si](C)(C)OC(=O)CC[C@@](O)(CC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C1849.4Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,3TMS,#4C[Si](C)(C)OC(=O)C[C@@](CCC(=O)O)(O[Si](C)(C)C)C(=O)O[Si](C)(C)C1873.7Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,4TMS,#1C[Si](C)(C)OC(=O)CC[C@](CC(=O)O[Si](C)(C)C)(O[Si](C)(C)C)C(=O)O[Si](C)(C)C1918.5Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,1TBDMS,#1CC(C)(C)[Si](C)(C)OC(=O)CC[C@@](O)(CC(=O)O)C(=O)O2063.3Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,1TBDMS,#2CC(C)(C)[Si](C)(C)O[C@](CCC(=O)O)(CC(=O)O)C(=O)O2068.4Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,1TBDMS,#3CC(C)(C)[Si](C)(C)OC(=O)C[C@](O)(CCC(=O)O)C(=O)O2056.4Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,1TBDMS,#4CC(C)(C)[Si](C)(C)OC(=O)[C@@](O)(CCC(=O)O)CC(=O)O2035.6Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,2TBDMS,#1CC(C)(C)[Si](C)(C)OC(=O)CC[C@](CC(=O)O)(O[Si](C)(C)C(C)(C)C)C(=O)O2318.5Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,2TBDMS,#2CC(C)(C)[Si](C)(C)OC(=O)CC[C@@](O)(CC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O2332.6Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,2TBDMS,#3CC(C)(C)[Si](C)(C)OC(=O)CC[C@@](O)(CC(=O)O)C(=O)O[Si](C)(C)C(C)(C)C2324.8Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,2TBDMS,#4CC(C)(C)[Si](C)(C)OC(=O)C[C@@](CCC(=O)O)(O[Si](C)(C)C(C)(C)C)C(=O)O2309.9Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,2TBDMS,#5CC(C)(C)[Si](C)(C)OC(=O)[C@@](CCC(=O)O)(CC(=O)O)O[Si](C)(C)C(C)(C)C2302.3Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,2TBDMS,#6CC(C)(C)[Si](C)(C)OC(=O)C[C@](O)(CCC(=O)O)C(=O)O[Si](C)(C)C(C)(C)C2331.1Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,3TBDMS,#1CC(C)(C)[Si](C)(C)OC(=O)CC[C@](CC(=O)O[Si](C)(C)C(C)(C)C)(O[Si](C)(C)C(C)(C)C)C(=O)O2573.2Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,3TBDMS,#2CC(C)(C)[Si](C)(C)OC(=O)CC[C@](CC(=O)O)(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2554.3Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,3TBDMS,#3CC(C)(C)[Si](C)(C)OC(=O)CC[C@@](O)(CC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2543.8Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,3TBDMS,#4CC(C)(C)[Si](C)(C)OC(=O)C[C@@](CCC(=O)O)(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2555.3Semi standard non polarhttps://arxiv.org/abs/1905.12712
Homocitric acid,4TBDMS,#1CC(C)(C)[Si](C)(C)OC(=O)CC[C@](CC(=O)O[Si](C)(C)C(C)(C)C)(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2756.5Semi standard non polarhttps://arxiv.org/abs/1905.12712
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Homocitric acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-0fsr-2900000000-1b6221744212821d13a42016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Homocitric acid GC-MS (4 TMS) - 70eV, Positivesplash10-004i-6039700000-bbcdc859874cb31d16db2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Homocitric acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Homocitric acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Homocitric acid 10V, Positive-QTOFsplash10-06ya-0910000000-10ce2a6c7dde8f6414f92016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Homocitric acid 20V, Positive-QTOFsplash10-03kc-6900000000-cc774f0962c580270a862016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Homocitric acid 40V, Positive-QTOFsplash10-0gb9-3900000000-1dbf32a3d216327d832a2016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Homocitric acid 10V, Negative-QTOFsplash10-08fr-1910000000-24186d115834b7a982192016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Homocitric acid 20V, Negative-QTOFsplash10-07vi-3900000000-78ce979f1c8cb053a6d22016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Homocitric acid 40V, Negative-QTOFsplash10-0aor-9600000000-dc1759e8907b4db138bd2016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Homocitric acid 10V, Negative-QTOFsplash10-07wl-1910000000-93d90a9e9b47624dde712021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Homocitric acid 20V, Negative-QTOFsplash10-014r-2900000000-10b9bd64cc7e5be410002021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Homocitric acid 40V, Negative-QTOFsplash10-00ku-9800000000-3926d2bdbaae258309362021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Homocitric acid 10V, Positive-QTOFsplash10-052u-0930000000-b304c640e74bcbd68b822021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Homocitric acid 20V, Positive-QTOFsplash10-0a4i-9200000000-f4181d391bb21114c3e12021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Homocitric acid 40V, Positive-QTOFsplash10-0a4i-9200000000-28608fc4dea9afb513542021-09-25Wishart 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 (predicted from logP)
Biospecimen Locations
  • Feces
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023186
KNApSAcK IDNot Available
Chemspider ID388564
KEGG Compound IDC01251
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkHomocitric acid
METLIN ID6943
PubChem Compound439459
PDB IDNot Available
ChEBI ID52222
Food Biomarker OntologyNot Available
VMH IDHCIT
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Boulat O, Gradwohl M, Matos V, Guignard JP, Bachmann C: Organic acids in the second morning urine in a healthy Swiss paediatric population. Clin Chem Lab Med. 2003 Dec;41(12):1642-58. [PubMed:14708889 ]
  2. van Rooyen JP, Mienie LJ, Erasmus E, de Wet WJ, Duran M, Wadman SK: Urinary excretion of homocitric acid and methylhomocitric acid in propionic acidaemia: minor metabolic products of the citrate synthase aldol condensation reaction. Clin Chim Acta. 1994 Oct 14;230(1):91-9. [PubMed:7850997 ]
  3. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Enzymes

General function:
Involved in metabolic process
Specific function:
Catalyzes the isomerization of citrate to isocitrate via cis-aconitate (By similarity).
Gene Name:
ACO2
Uniprot ID:
Q99798
Molecular weight:
85424.745
Reactions
Homocitric acid → (Z)-But-1-ene-1,2,4-tricarboxylate + Waterdetails
General function:
Involved in metabolic process
Specific function:
Iron sensor. Binds a 4Fe-4S cluster and functions as aconitase when cellular iron levels are high. Functions as mRNA binding protein that regulates uptake, sequestration and utilization of iron when cellular iron levels are low. Binds to iron-responsive elements (IRES) in target mRNA species when iron levels are low. Binding of a 4Fe-4S cluster precludes RNA binding. Catalyzes the isomerization of citrate to isocitrate via cis-aconitate (By similarity).
Gene Name:
ACO1
Uniprot ID:
P21399
Molecular weight:
98398.14
Reactions
Homocitric acid → (Z)-But-1-ene-1,2,4-tricarboxylate + Waterdetails