MiMeDB: Showing metabocard for (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate (MMDBc0031738)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:47:11 UTC

Update Date

2022-08-31 18:24:06 UTC

Metabolite ID

MMDBc0031738

Metabolite Identification

Common Name

(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate

Description

Tricarboxylate anion of (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylic acid

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241222492D          

 14 13  0  0  1  0            999 V2000
   -0.1914   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5230   -1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914   -2.3645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -2.3645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6500   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  2  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
  6 12  1  1  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031738

> <DATABASE_NAME>
MIME

> <SMILES>
C[C@H](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)/t3-,7+/m1/s1

> <INCHI_KEY>
YNOXCRMFGMSKIJ-NFNCENRGSA-N

> <FORMULA>
C7H10O7

> <MOLECULAR_WEIGHT>
206.1501

> <EXACT_MASS>
206.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
17.326490002168775

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S)-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>
132.13000000000002

> <JCHEM_REFRACTIVITY>
40.1984

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.75e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S)-2-methylcitric acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -0.357  -1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976  -2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.976  -3.644   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.357  -4.414   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       2.310  -4.414   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.080  -2.667   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       3.644  -0.564   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.977  -1.334   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.311  -0.564   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.977  -2.874   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.310   1.334   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    2    7    8   12                                             
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    6   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Synonyms

Value	Source
(2S,3S)-2-Hydroxybutane-1,2,3-tricarboxylic acid	Generator
(2S,3S)-2-Methylcitrate	Generator
2-Methylcitrate	MeSH
Methylcitric acid	MeSH
2-Methylcitric acid	MeSH
3-Carboxy-3-hydroxy-2-methylpentanedioic acid	MeSH
2-Methylcitric acid, 3H-labeled	MeSH

Molecular Formula

C₇H₁₀O₇

Average Mass

206.1501

Monoisotopic Mass

206.042652674

IUPAC Name

(1S,2S)-2-hydroxy-1-methylpropane-1,2,3-tricarboxylic acid

Traditional Name

(2S,3S)-2-methylcitric acid

CAS Registry Number

Not Available

SMILES

C[C@H](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)/t3-,7+/m1/s1

InChI Key

YNOXCRMFGMSKIJ-NFNCENRGSA-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

2-methylcitric acid (CHEBI:50948 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	175 g/L	ALOGPS
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	17.33 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	splash10-0fer-4900000000-66b99961c9a1426fcc9e	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0900000000-be0da5c29220e9e50325	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-05i0-9600000000-2bead66ba2514df6497f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-1093-7900000000-e7a5530b8562d859e032	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0900-1910000000-0a84eb8e0df2e6eb450d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-07vi-4900000000-e89ea7de4d7e433cae1e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9300000000-c68ffdf8bf6f5380005e	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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
MMDBr0013680	(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate	2-methyl-cis-aconitic acid	2-methylcitrate dehydratase	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0014382	Water	(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate	2-methylcitrate synthase	Synthesis	RHEA	34755880
MMDBr0014652	(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate	2-methyl-trans-aconitic acid	2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)	Hydration/dehydration of C-O bond	RHEA	34755880

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	5	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Bacteria/NULL	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Bacteria	Actinobacteria	3	Human
Eukaryota/Fungi	Ascomycota	8	Human feces; Human saliva	Unknown
Bacteria	nah	1

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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12898022

PDB ID

Not Available

ChEBI ID

50948

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate (MMDBc0031738)

MOL for #<Metabolite:0x00007fe2d6c81480>

3D MOL for #<Metabolite:0x00007fe2d6c81480>

3D SDF for #<Metabolite:0x00007fe2d6c81480>

3D-SDF for #<Metabolite:0x00007fe2d6c81480>

PDB for #<Metabolite:0x00007fe2d6c81480>

3D PDB for #<Metabolite:0x00007fe2d6c81480>

SMILES for #<Metabolite:0x00007fe2d6c81480>

INCHI for #<Metabolite:0x00007fe2d6c81480>

Structure for #<Metabolite:0x00007fe2d6c81480>

3D Structure for #<Metabolite:0x00007fe2d6c81480>