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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2006-08-12 22:40:07 UTC

Update Date

2023-02-21 17:16:43 UTC

HMDB ID

HMDB0003518

Secondary Accession Numbers

HMDB03518

Metabolite Identification

Common Name

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>
HMDB0003518

> <DATABASE_NAME>
hmdb

> <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

View in JSmol View NMR Assignments View Stereo Labels

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

Chemical Formula

C₇H₁₀O₇

Average Molecular Weight

206.1501

Monoisotopic Molecular Weight

206.042652674

IUPAC Name

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

Traditional Name

(R)-homocitric acid

CAS Registry Number

13052-73-8

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 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 )

Ontology

Not Available

Placenta (HMDB: HMDB0003518)

Excreta

Biofluid or Excreta

Feces (PMID: 27543620)

Cellular substructure

Cytoplasm (HMDB: HMDB0003518)

Source

Endogenous

Endogenous (HMDB: HMDB0003518)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Pyruvate Metabolism (PathBank: SMP0002355)
Lysine Metabolism (PathBank: SMP0002337)

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	Not Available	129.995	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000061

Predicted Molecular 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	145.715	31661259
DarkChem	[M-H]-	137.886	31661259
DeepCCS	[M+H]+	134.983	30932474
DeepCCS	[M-H]-	132.587	30932474
DeepCCS	[M-2H]-	167.637	30932474
DeepCCS	[M+Na]+	142.985	30932474
AllCCS	[M+H]+	144.5	32859911
AllCCS	[M+H-H2O]+	140.9	32859911
AllCCS	[M+NH4]+	147.9	32859911
AllCCS	[M+Na]+	148.8	32859911
AllCCS	[M-H]-	138.4	32859911
AllCCS	[M+Na-2H]-	139.4	32859911
AllCCS	[M+HCOO]-	140.5	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	1.47 minutes	32390414
Predicted by Siyang on May 30, 2022	9.9119 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	7.1 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	308.7 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	662.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	301.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	47.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	170.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	59.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	254.9 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	252.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	582.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	600.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	57.4 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	871.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	187.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	228.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	779.2 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	257.2 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	617.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Homocitric acid	OC(=O)CC[C@@](O)(CC(O)=O)C(O)=O	2956.1	Standard polar	33892256
Homocitric acid	OC(=O)CC[C@@](O)(CC(O)=O)C(O)=O	1271.1	Standard non polar	33892256
Homocitric acid	OC(=O)CC[C@@](O)(CC(O)=O)C(O)=O	1852.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Homocitric acid,1TMS,isomer #1	C[Si](C)(C)OC(=O)CC[C@@](O)(CC(=O)O)C(=O)O	1780.4	Semi standard non polar	33892256
Homocitric acid,1TMS,isomer #2	C[Si](C)(C)O[C@](CCC(=O)O)(CC(=O)O)C(=O)O	1831.0	Semi standard non polar	33892256
Homocitric acid,1TMS,isomer #3	C[Si](C)(C)OC(=O)C[C@](O)(CCC(=O)O)C(=O)O	1781.9	Semi standard non polar	33892256
Homocitric acid,1TMS,isomer #4	C[Si](C)(C)OC(=O)[C@@](O)(CCC(=O)O)CC(=O)O	1728.1	Semi standard non polar	33892256
Homocitric acid,2TMS,isomer #1	C[Si](C)(C)OC(=O)CC[C@](CC(=O)O)(O[Si](C)(C)C)C(=O)O	1860.2	Semi standard non polar	33892256
Homocitric acid,2TMS,isomer #2	C[Si](C)(C)OC(=O)CC[C@@](O)(CC(=O)O[Si](C)(C)C)C(=O)O	1855.8	Semi standard non polar	33892256
Homocitric acid,2TMS,isomer #3	C[Si](C)(C)OC(=O)CC[C@@](O)(CC(=O)O)C(=O)O[Si](C)(C)C	1805.3	Semi standard non polar	33892256
Homocitric acid,2TMS,isomer #4	C[Si](C)(C)OC(=O)C[C@@](CCC(=O)O)(O[Si](C)(C)C)C(=O)O	1853.3	Semi standard non polar	33892256
Homocitric acid,2TMS,isomer #5	C[Si](C)(C)OC(=O)[C@@](CCC(=O)O)(CC(=O)O)O[Si](C)(C)C	1836.1	Semi standard non polar	33892256
Homocitric acid,2TMS,isomer #6	C[Si](C)(C)OC(=O)C[C@](O)(CCC(=O)O)C(=O)O[Si](C)(C)C	1814.2	Semi standard non polar	33892256
Homocitric acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)CC[C@](CC(=O)O[Si](C)(C)C)(O[Si](C)(C)C)C(=O)O	1865.3	Semi standard non polar	33892256
Homocitric acid,3TMS,isomer #2	C[Si](C)(C)OC(=O)CC[C@](CC(=O)O)(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1884.8	Semi standard non polar	33892256
Homocitric acid,3TMS,isomer #3	C[Si](C)(C)OC(=O)CC[C@@](O)(CC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1849.4	Semi standard non polar	33892256
Homocitric acid,3TMS,isomer #4	C[Si](C)(C)OC(=O)C[C@@](CCC(=O)O)(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1873.7	Semi standard non polar	33892256
Homocitric acid,4TMS,isomer #1	C[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)C	1918.5	Semi standard non polar	33892256
Homocitric acid,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CC[C@@](O)(CC(=O)O)C(=O)O	2063.3	Semi standard non polar	33892256
Homocitric acid,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@](CCC(=O)O)(CC(=O)O)C(=O)O	2068.4	Semi standard non polar	33892256
Homocitric acid,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)C[C@](O)(CCC(=O)O)C(=O)O	2056.4	Semi standard non polar	33892256
Homocitric acid,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC(=O)[C@@](O)(CCC(=O)O)CC(=O)O	2035.6	Semi standard non polar	33892256
Homocitric acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CC[C@](CC(=O)O)(O[Si](C)(C)C(C)(C)C)C(=O)O	2318.5	Semi standard non polar	33892256
Homocitric acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CC[C@@](O)(CC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O	2332.6	Semi standard non polar	33892256
Homocitric acid,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)CC[C@@](O)(CC(=O)O)C(=O)O[Si](C)(C)C(C)(C)C	2324.8	Semi standard non polar	33892256
Homocitric acid,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC(=O)C[C@@](CCC(=O)O)(O[Si](C)(C)C(C)(C)C)C(=O)O	2309.9	Semi standard non polar	33892256
Homocitric acid,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)OC(=O)[C@@](CCC(=O)O)(CC(=O)O)O[Si](C)(C)C(C)(C)C	2302.3	Semi standard non polar	33892256
Homocitric acid,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)OC(=O)C[C@](O)(CCC(=O)O)C(=O)O[Si](C)(C)C(C)(C)C	2331.1	Semi standard non polar	33892256
Homocitric acid,3TBDMS,isomer #1	CC(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	2573.2	Semi standard non polar	33892256
Homocitric acid,3TBDMS,isomer #2	CC(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)C	2554.3	Semi standard non polar	33892256
Homocitric acid,3TBDMS,isomer #3	CC(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)C	2543.8	Semi standard non polar	33892256
Homocitric acid,3TBDMS,isomer #4	CC(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)C	2555.3	Semi standard non polar	33892256
Homocitric acid,4TBDMS,isomer #1	CC(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)C	2756.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Homocitric acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fsr-2900000000-1b6221744212821d13a4	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Homocitric acid GC-MS (4 TMS) - 70eV, Positive	splash10-004i-6039700000-bbcdc859874cb31d16db	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Homocitric acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Homocitric acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Homocitric acid 10V, Positive-QTOF	splash10-06ya-0910000000-10ce2a6c7dde8f6414f9	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Homocitric acid 20V, Positive-QTOF	splash10-03kc-6900000000-cc774f0962c580270a86	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Homocitric acid 40V, Positive-QTOF	splash10-0gb9-3900000000-1dbf32a3d216327d832a	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Homocitric acid 10V, Negative-QTOF	splash10-08fr-1910000000-24186d115834b7a98219	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Homocitric acid 20V, Negative-QTOF	splash10-07vi-3900000000-78ce979f1c8cb053a6d2	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Homocitric acid 40V, Negative-QTOF	splash10-0aor-9600000000-dc1759e8907b4db138bd	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Homocitric acid 10V, Negative-QTOF	splash10-07wl-1910000000-93d90a9e9b47624dde71	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Homocitric acid 20V, Negative-QTOF	splash10-014r-2900000000-10b9bd64cc7e5be41000	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Homocitric acid 40V, Negative-QTOF	splash10-00ku-9800000000-3926d2bdbaae25830936	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Homocitric acid 10V, Positive-QTOF	splash10-052u-0930000000-b304c640e74bcbd68b82	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Homocitric acid 20V, Positive-QTOF	splash10-0a4i-9200000000-f4181d391bb21114c3e1	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Homocitric acid 40V, Positive-QTOF	splash10-0a4i-9200000000-28608fc4dea9afb51354	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm (predicted from logP)

Biospecimen Locations

Blood
Feces
Urine

Tissue Locations

Placenta

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	27543620	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

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

VMH ID

HCIT

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]
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 ]
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

Enzyme Details

1. Aconitate hydratase, mitochondrial

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 + Water	details

Enzyme Details

2. Cytoplasmic aconitate hydratase

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 + Water	details

Showing metabocard for Homocitric acid (HMDB0003518)

MOL for HMDB0003518 (Homocitric acid)

3D MOL for HMDB0003518 (Homocitric acid)

3D SDF for HMDB0003518 (Homocitric acid)

3D-SDF for HMDB0003518 (Homocitric acid)

PDB for HMDB0003518 (Homocitric acid)

3D PDB for HMDB0003518 (Homocitric acid)

SMILES for HMDB0003518 (Homocitric acid)

INCHI for HMDB0003518 (Homocitric acid)

Structure for HMDB0003518 (Homocitric acid)

3D Structure for HMDB0003518 (Homocitric acid)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra

Enzymes

Reactions

Reactions