MiMeDB: Showing metabocard for (2R)-Homocitric acid (MMDBc0032919)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:27:22 UTC

Update Date

2024-04-30 19:54:59 UTC

Metabolite ID

MMDBc0032919

Metabolite Identification

Common Name

(2R)-Homocitric acid

Description

Homocitric 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

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


  Mrv1652310231917012D          

 14 13  0  0  0  0            999 V2000
 9993.1424 9992.7759    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9992.4284 9993.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9991.7139 9992.7759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9990.9992 9993.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9990.2846 9992.7759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.9992 9994.0128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.8577 9993.1882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.5730 9992.7759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.2863 9993.1882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9994.5730 9991.9517    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.1424 9991.9517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9993.8577 9991.5381    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9992.4284 9991.5381    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.8577 9992.3634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  1 11  1  0  0  0  0
  1 14  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0032919

> <DATABASE_NAME>
MIME

> <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_KEY>
XKJVEVRQMLKSMO-SSDOTTSWSA-N

> <FORMULA>
C7H10O7

> <MOLECULAR_WEIGHT>
206.1501

> <EXACT_MASS>
206.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
17.44345390081851

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-hydroxybutane-1,2,4-tricarboxylic acid

> <ALOGPS_LOGP>
-1.50

> <JCHEM_LOGP>
-1.0340262470000003

> <ALOGPS_LOGS>
-0.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.9251914717112886

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.086703991163821

> <JCHEM_PKA_STRONGEST_BASIC>
-4.0751445556736625

> <JCHEM_POLAR_SURFACE_AREA>
132.13

> <JCHEM_REFRACTIVITY>
40.37890000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.91e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(R)-homocitric acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-OCT-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-OCT-19         0                                  
HETATM    1  C   UNK     0    8653.8668653.182   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8652.5338653.951   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8651.1998653.182   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8649.8658653.951   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8648.5318653.182   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8649.8658655.491   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8655.2018653.951   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8656.5368653.182   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0    8657.8688653.951   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8656.5368651.643   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0    8653.8668651.643   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0    8655.2018650.871   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0    8652.5338650.871   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0    8655.2018652.412   0.000  0.00  0.00           O+0
CONECT    1    2    7   11   14                                             
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    1    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    1   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    1                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Synonyms

Value	Source
(R)-2-Hydroxy-1,2,4-butanetricarboxylic acid	ChEBI
(R)-2-Hydroxybutane-1,2,4-tricarboxylic acid	ChEBI
(R)-Homocitric acid	ChEBI
3-Hydroxy-3-carboxyadipic acid	ChEBI
Homocitrate	ChEBI
(R)-2-Hydroxy-1,2,4-butanetricarboxylate	Generator
(R)-2-Hydroxybutane-1,2,4-tricarboxylate	Generator
(R)-Homocitrate	Generator
3-Hydroxy-3-carboxyadipate	Generator
2-Hydroxybutane-1,2,4-tricarboxylate	HMDB
(2R)-2-Hydroxy-1,2,4-butanetricarboxylate	HMDB
(2R)-2-Hydroxy-1,2,4-butanetricarboxylic acid	HMDB
(±)-homocitrate	HMDB
(±)-homocitric acid	HMDB
2-Hydroxy-1,2,4-butanetricarboxylate	HMDB
2-Hydroxy-1,2,4-butanetricarboxylic acid	HMDB
Homocitric acid	HMDB

Molecular Formula

C₇H₁₀O₇

Average Mass

206.1501

Monoisotopic Mass

206.042652674

IUPAC Name

(2R)-2-hydroxybutane-1,2,4-tricarboxylic acid

Traditional Name

(R)-homocitric acid

CAS Registry Number

3562-74-1

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 Key

XKJVEVRQMLKSMO-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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Tricarboxylic acids and derivatives

Direct Parent

Tricarboxylic 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 Framework

Aliphatic acyclic compounds

External Descriptors

homocitric acid (CHEBI:52222 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	191 g/L	ALOGPS
logP	-1.5	ALOGPS
logP	-1	ChemAxon
logS	-0.03	ALOGPS
pKa (Strongest Acidic)	3.09	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	132.13 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	40.38 m³·mol⁻¹	ChemAxon
Polarizability	17.44 Å³	ChemAxon
Number of Rings	0	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
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fsr-2900000000-1b6221744212821d13a4	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-004i-6039700000-bbcdc859874cb31d16db	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
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-06ya-0910000000-10ce2a6c7dde8f6414f9	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03kc-6900000000-cc774f0962c580270a86	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0gb9-3900000000-1dbf32a3d216327d832a	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-08fr-1910000000-24186d115834b7a98219	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-07vi-3900000000-78ce979f1c8cb053a6d2	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0aor-9600000000-dc1759e8907b4db138bd	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-07wl-1910000000-93d90a9e9b47624dde71	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014r-2900000000-10b9bd64cc7e5be41000	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00ku-9800000000-3926d2bdbaae25830936	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-052u-0930000000-b304c640e74bcbd68b82	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4i-9200000000-f4181d391bb21114c3e1	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9200000000-28608fc4dea9afb51354	2021-09-25	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

Feces
Placenta

Tissue Locations

Placenta

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0192363	Aconitate hydratase, mitochondrial	Enzyme	Q99798	Homo sapiens
MMDBp0192364	Cytoplasmic aconitate hydratase	Unknown	P21399	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0008191	Oxoglutaric acid	(2R)-Homocitric acid	Not Available		VMH	30371894

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	7	Human feces; Human saliva	Unknown
Bacteria	Proteobacteria	23	Human ; Human feces; Human sputum; Human unknown; Human subgingival plaque	Metabolic reconstruction
Bacteria	Firmicutes	27	Human feces; Human	Metabolic reconstruction
Bacteria	Bacteroidetes	3	Human feces	Metabolic reconstruction
Bacteria	Candidatus melainabacteria	1	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	1		Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Archaea/Archaea	Euryarchaeota	7		Metabolic reconstruction
Archaea/Archaea	Crenarchaeota	8		Metabolic reconstruction
Bacteria	Deinococcus-thermus	1
Bacteria	Actinobacteria	2
Bacteria	Cyanobacteria	1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified				HMDB
Human Placenta	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	27543620

External Links

HMDB ID

HMDB0003518

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023186

KNApSAcK ID

Not Available

Chemspider ID

388564

KEGG Compound ID

C01251

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Homocitric acid

METLIN ID

6943

PubChem Compound

439459

PDB ID

Not Available

ChEBI ID

52222

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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. doi: 10.1016/0009-8981(94)90092-2. [PubMed:7850997 ]
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. doi: 10.1515/CCLM.2003.248. [PubMed:14708889 ]
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 ]

Showing metabocard for (2R)-Homocitric acid (MMDBc0032919)

MOL for #<Metabolite:0x00007fecc0011940>

3D MOL for #<Metabolite:0x00007fecc0011940>

3D SDF for #<Metabolite:0x00007fecc0011940>

3D-SDF for #<Metabolite:0x00007fecc0011940>

PDB for #<Metabolite:0x00007fecc0011940>

3D PDB for #<Metabolite:0x00007fecc0011940>

SMILES for #<Metabolite:0x00007fecc0011940>

INCHI for #<Metabolite:0x00007fecc0011940>

Structure for #<Metabolite:0x00007fecc0011940>

3D Structure for #<Metabolite:0x00007fecc0011940>