NP-MRD: Showing NP-Card for 2-Methylcitric acid (NP0086566)

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Record Information

Version

2.0

Created at

2022-05-11 16:24:38 UTC

Updated at

2022-05-11 16:24:38 UTC

NP-MRD ID

NP0086566

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-Methylcitric acid

Description

2-Methylcitric acid, also known as 2-methylcitrate, belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. 2-Methylcitric acid is an extremely weak basic (essentially neutral) compound (based on its pKa). 2-Methylcitric acid exists in all living organisms, ranging from bacteria to humans. Outside of the human body, 2-Methylcitric acid has been detected, but not quantified in, milk (cow). This could make 2-methylcitric acid a potential biomarker for the consumption of these foods. 2-Methylcitric acid is a potentially toxic compound. 2-Methylcitric acid is found in Apis cerana and Schisandra chinensis. 2-Methylcitric acid was first documented in 1981 (PMID: 7313494). 2-Methylcitric acid, with regard to humans, has been found to be associated with several diseases such as crohn's disease and iron deficiency; 2-methylcitric acid has also been linked to several inborn metabolic disorders including isovaleric acidemia, vitamin B12 deficiency, and propionic acidemia (PMID: 8345822) (PMID: 12113988).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02231218292D          

 14 13  0  0  0  0            999 V2000
    8.8380   -4.9115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9005   -5.6260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2505   -5.6260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3130   -6.3404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8380   -6.3404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0755   -4.8009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0755   -5.6260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9005   -7.0549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1379   -6.3404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0130   -6.3404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2505   -7.0549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7900   -4.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3610   -4.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.0755   -6.4509    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  2  7  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  0  0  0  0
  5 11  2  0  0  0  0
  6  7  1  0  0  0  0
  6 12  1  0  0  0  0
  6 13  2  0  0  0  0
  7 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0086566

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C(O)=O)C(O)(CC(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H10O7/c1-3(5(10)11)7(14,6(12)13)2-4(8)9/h3,14H,2H2,1H3,(H,8,9)(H,10,11)(H,12,13)

> <INCHI_KEY>
YNOXCRMFGMSKIJ-UHFFFAOYSA-N

> <FORMULA>
C7H10O7

> <MOLECULAR_WEIGHT>
206.1501

> <EXACT_MASS>
206.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
17.21399595260961

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxy-1-methylpropane-1,2,3-tricarboxylic acid

> <ALOGPS_LOGP>
-0.89

> <JCHEM_LOGP>
-0.7797011736666666

> <ALOGPS_LOGS>
-0.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
4.7852796669207125

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.18324322639043

> <JCHEM_PKA_STRONGEST_BASIC>
-4.260390633991254

> <JCHEM_POLAR_SURFACE_AREA>
132.13

> <JCHEM_REFRACTIVITY>
40.19840000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.75e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylcitric acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      16.498  -9.168   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      20.348 -10.502   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      17.268 -10.502   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      21.118 -11.835   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.498 -11.835   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.808  -8.962   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      18.808 -10.502   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      20.348 -13.169   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      22.657 -11.835   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      14.958 -11.835   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      17.268 -13.169   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      20.141  -8.192   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      17.474  -8.192   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      18.808 -12.042   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2    7    4                                                       
CONECT    3    1    5    7                                                  
CONECT    4    2    8    9                                                  
CONECT    5    3   10   11                                                  
CONECT    6    7   12   13                                                  
CONECT    7    2    3    6   14                                             
CONECT    8    4                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    6                                                            
CONECT   14    7                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

View in JSmol

Synonyms

Value	Source
2-Hydroxy-1,2,3-butanetricarboxylic acid	ChEBI
2-Hydroxy-1,2,3-butanetricarboxylate	Generator
2-Methylcitrate	Generator
(2S,3S)-2-Methylcitrate	HMDB
2-Hydroxybutane-1,2,3-tricarboxylate	HMDB
2-Hydroxybutane-1,2,3-tricarboxylic acid	HMDB
2-Methylcitric acid, 3H-labeled	HMDB
3-Carboxy-3-hydroxy-2-methylpentanedioic acid	HMDB
Methylcitric acid	HMDB

Chemical Formula

C₇H₁₀O₇

Average Mass

206.1501 Da

Monoisotopic Mass

206.04265 Da

IUPAC Name

2-hydroxy-1-methylpropane-1,2,3-tricarboxylic acid

Traditional Name

methylcitric acid

CAS Registry Number

Not Available

SMILES

CC(C(O)=O)C(O)(CC(O)=O)C(O)=O

InChI Identifier

InChI=1S/C7H10O7/c1-3(5(10)11)7(14,6(12)13)2-4(8)9/h3,14H,2H2,1H3,(H,8,9)(H,10,11)(H,12,13)

InChI Key

YNOXCRMFGMSKIJ-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Apis cerana	LOTUS Database	35616633
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Schisandra chinensis	LOTUS Database	35616633
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

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

tricarboxylic acid (CHEBI:30835 )

Physical Properties

State

Not Available

Experimental 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

Predicted Properties

Property	Value	Source
logP	-0.89	ALOGPS
logP	-0.78	ChemAxon
logS	-0.07	ALOGPS
pKa (Strongest Acidic)	3.18	ChemAxon
pKa (Strongest Basic)	-4.3	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	5	ChemAxon
Refractivity	40.2 m³·mol⁻¹	ChemAxon
Polarizability	17.21 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

External Links

HMDB ID

HMDB0000379

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB021997

KNApSAcK ID

Not Available

Chemspider ID

500

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

39369

Wikipedia Link

Not Available

METLIN ID

5368

PubChem Compound

515

PDB ID

Not Available

ChEBI ID

30835

Good Scents ID

Not Available

References

General References

Allen RH, Stabler SP, Savage DG, Lindenbaum J: Elevation of 2-methylcitric acid I and II levels in serum, urine, and cerebrospinal fluid of patients with cobalamin deficiency. Metabolism. 1993 Aug;42(8):978-88. [PubMed:8345822 ]
Bergstrom T, Greter J, Levin AH, Steen G, Tryding N, Wass U: Propionyl-CoA carboxylase deficiency: case report, effect of low-protein diet and identification of 3-oxo-2-methylvaleric acid 3-hydroxy-2-methylvaleric acid, and maleic acid in urine. Scand J Clin Lab Invest. 1981 Apr;41(2):117-26. [PubMed:7313494 ]
Busch M, Stein G, Poppitz W, Hein G, Muller A: Validated capillary gas chromatographic-mass spectrometric assay to determine 2-methylcitric acid I and II levels in human serum by using a pulsed splitless injection procedure. J Chromatogr B Analyt Technol Biomed Life Sci. 2002 Aug 5;775(2):215-23. doi: 10.1016/s1570-0232(02)00293-3. [PubMed:12113988 ]

Showing NP-Card for 2-Methylcitric acid (NP0086566)

MOL for NP0086566 (2-Methylcitric acid)

3D MOL for NP0086566 (2-Methylcitric acid)

3D SDF for NP0086566 (2-Methylcitric acid)

3D-SDF for NP0086566 (2-Methylcitric acid)

PDB for NP0086566 (2-Methylcitric acid)

3D PDB for NP0086566 (2-Methylcitric acid)

SMILES for NP0086566 (2-Methylcitric acid)

INCHI for NP0086566 (2-Methylcitric acid)

Structure for NP0086566 (2-Methylcitric acid)

3D Structure for NP0086566 (2-Methylcitric acid)