MiMeDB: Showing metabocard for Methylisocitric acid (MMDBc0029833)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:43:33 UTC

Update Date

2022-08-31 17:19:11 UTC

Metabolite ID

MMDBc0029833

Metabolite Identification

Common Name

Methylisocitric acid

Description

Methylisocitric acid is a product of bacterial metabolism in the gut. It can be produced by 2-methylisocitrate lyase and by 2-methylisocitrate dehydratase.

Structure

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


  Mrv0541 02231220402D          

 14 13  0  0  0  0            999 V2000
   14.2316  -12.9572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.7875  -13.2592    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.2152  -13.6715    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0730  -14.4967    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9296  -14.9092    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0730  -11.1967    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.7875  -12.4342    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3585  -13.2592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6440  -13.6715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3585  -12.4342    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0566  -14.3860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0730  -13.6715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9296  -14.0842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0730  -12.0216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2 12  1  0  0  0  0
  3 13  1  0  0  0  0
  4 12  2  0  0  0  0
  5 13  2  0  0  0  0
  6 14  1  0  0  0  0
  7 14  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  8 12  1  0  0  0  0
  9 11  1  0  0  0  0
  9 13  1  0  0  0  0
 10 14  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029833

> <DATABASE_NAME>
MIME

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

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

> <INCHI_KEY>
HHKPKXCSHMJWCF-UHFFFAOYSA-N

> <FORMULA>
C7H10O7

> <MOLECULAR_WEIGHT>
206.1501

> <EXACT_MASS>
206.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
17.369726498071245

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.87

> <JCHEM_LOGP>
-1.0135623636666664

> <ALOGPS_LOGS>
-0.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
4.805179537739238

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1668703375685876

> <JCHEM_PKA_STRONGEST_BASIC>
-4.066922204255973

> <JCHEM_POLAR_SURFACE_AREA>
132.13

> <JCHEM_REFRACTIVITY>
40.42940000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.49e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
α-methylisocitric 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  O   UNK     0      26.566 -24.187   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      31.337 -24.750   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      24.668 -25.520   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      30.003 -27.061   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      26.002 -27.830   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      30.003 -20.901   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      31.337 -23.210   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      28.669 -24.750   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      27.335 -25.520   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      28.669 -23.210   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      28.106 -26.854   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      30.003 -25.520   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      26.002 -26.290   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      30.003 -22.440   0.000  0.00  0.00           C+0
CONECT    1    9                                                            
CONECT    2   12                                                            
CONECT    3   13                                                            
CONECT    4   12                                                            
CONECT    5   13                                                            
CONECT    6   14                                                            
CONECT    7   14                                                            
CONECT    8    9   10   12                                                  
CONECT    9    1    8   11   13                                             
CONECT   10    8   14                                                       
CONECT   11    9                                                            
CONECT   12    2    4    8                                                  
CONECT   13    3    5    9                                                  
CONECT   14    6    7   10                                                  
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Synonyms

Value	Source
3-Carboxy-2,3-dideoxy-4-C-methylpentaric acid	ChEBI
alpha-Methylisocitric acid	ChEBI
3-Carboxy-2,3-dideoxy-4-C-methylpentarate	Generator
a-Methylisocitrate	Generator
a-Methylisocitric acid	Generator
alpha-Methylisocitrate	Generator
Α-methylisocitrate	Generator
Α-methylisocitric acid	Generator
Methylisocitrate	Generator
3-Hydroxy-1,2,3-butanetricarboxylate	MeSH
DL-Threo-alpha-methylisocitrate	MeSH
Threo-alpha-methylisocitrate, (3)H-labeled	MeSH
(2R,3S)2-Methylisocitrate	HMDB
(2S,3R)-3-Hydroxybutane-1,2,3-tricarboxylate	HMDB
3-Hydroxy-1,2,3-butanetricarboxylic acid	HMDB
3-Hydroxybutane-1,2,3-tricarboxylic acid	HMDB
D.L-methylisocitrate	HMDB
DL-Methylisocitric acid	HMDB
threo-alpha-Methylisocitrate	HMDB, MeSH

Molecular Formula

C₇H₁₀O₇

Average Mass

206.1501

Monoisotopic Mass

206.042652674

IUPAC Name

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

Traditional Name

α-methylisocitric acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

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

InChI Key

HHKPKXCSHMJWCF-UHFFFAOYSA-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

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	149 g/L	ALOGPS
logP	-0.87	ALOGPS
logP	-1	ChemAxon
logS	-0.14	ALOGPS
pKa (Strongest Acidic)	3.17	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	5	ChemAxon
Refractivity	40.43 m³·mol⁻¹	ChemAxon
Polarizability	17.37 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	splash10-000i-9700000000-5e955ef633a08113ea4b	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-004i-6237900000-699512d84d6d00556b85	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 LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000l-0900000000-f2ba7990914621684f43	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00xs-6900000000-56bcf049292c1d2aec9f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01bc-5900000000-5450b7d1dc2e0d752d8f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0909-2910000000-76e456521d06eb2df306	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014i-2900000000-9ff275785270b3b9744a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00di-9300000000-08a246451feb097e60ee	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0900000000-1f979af8cdefad8b7fc2	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014i-0900000000-72ddc9d43332ef4d4c1e	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-014l-7900000000-b552ff6cfa53a6d1478c	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000j-0910000000-69d3ffec30c69b150998	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0fxy-2900000000-cfe61511f4feda222931	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00di-9100000000-7f3760d40cf2db6bf9eb	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-16	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0007899	Methylisocitric acid	Pyruvic acid	Not Available	Methylisocitrate lyase	VMH	30371894
MMDBr0007905	Cis-2-Methylaconitate	Methylisocitric acid	Not Available	2-Methylisocitrate Dehydratase	VMH	30371894
MMDBr0008512	Cis-2-Methylaconitate	Methylisocitric acid	Not Available	2-methylisocitrate dehydratase	VMH	30371894
MMDBr0018588	Cis-2-Methylaconitate	Water	Aconitate hydratase B	Hydration/dehydration of C-O bond	PathBank	31602464
MMDBr0018589	Methylisocitric acid	Pyruvic acid	2-methylisocitrate lyase	Non-hydrolytic bond cleavage (or its reversal)	PathBank	31602464

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
Bacteria	Proteobacteria	107	Human feces; Human sputum; Human ; Human unknown; Human pleural fluid plaque; Human stool; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	58	Human feces; Human	Metabolic reconstruction
Bacteria	Bacteroidetes	52	Human feces; Human appendix biopsy; Human ; Human gastric fluid; Human saliva; Human subgingival plaque; Human stool	Metabolic reconstruction
Bacteria	Synergistetes	3	Human feces	Metabolic reconstruction
Bacteria	Actinobacteria	47	Human feces; Human	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0006471

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023929

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

513

PDB ID

Not Available

ChEBI ID

142525

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for Methylisocitric acid (MMDBc0029833)

MOL for #<Metabolite:0x00007fe2ac010568>

3D MOL for #<Metabolite:0x00007fe2ac010568>

3D SDF for #<Metabolite:0x00007fe2ac010568>

3D-SDF for #<Metabolite:0x00007fe2ac010568>

PDB for #<Metabolite:0x00007fe2ac010568>

3D PDB for #<Metabolite:0x00007fe2ac010568>

SMILES for #<Metabolite:0x00007fe2ac010568>

INCHI for #<Metabolite:0x00007fe2ac010568>

Structure for #<Metabolite:0x00007fe2ac010568>

3D Structure for #<Metabolite:0x00007fe2ac010568>