MiMeDB: Showing metabocard for (2R,3S)-2-Hydroxybutane-1,2,3-tricarboxylate (MMDBc0031739)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:47:13 UTC

Update Date

2022-08-31 18:24:06 UTC

Metabolite ID

MMDBc0031739

Metabolite Identification

Common Name

(2R,3S)-2-Hydroxybutane-1,2,3-tricarboxylate

Description

(2R,3S)-2-Hydroxybutane-1,2,3-tricarboxylate is an intermediate in methylcitrate metabolism. It is involved in the reaction propinoyl-CoA + H2O + oxaloacetate = (2R,3S)-2-hydroxybutane-1,2,3-tricarboxylate + CoA which is mediated by the enzyme: 2-methylcitrate synthase.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 10101211142D          

 15 14  0  0  0  0            999 V2000
    1.5395   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -0.3020    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2539    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -0.3020    0.0000 C   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
    1.5395    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5395    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  1  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  7  2  1  0  0  0  0
  7  3  1  0  0  0  0
  7  6  1  1  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
 12  6  2  0  0  0  0
 13  6  1  0  0  0  0
  7 14  1  6  0  0  0
  3 15  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031739

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](C)(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-WVBDSBKLSA-N

> <FORMULA>
C7H10O7

> <MOLECULAR_WEIGHT>
206.1501

> <EXACT_MASS>
206.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
17.298318833954408

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R)-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>
4.785279666920712

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-OCT-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   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
HETATM   15  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    4    7                                                       
CONECT    3    1    5    7   15                                             
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                                                            
CONECT   15    3                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

Synonyms

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

Molecular Formula

C₇H₁₀O₇

Average Mass

206.1501

Monoisotopic Mass

206.042652674

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

[H][C@@](C)(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-WVBDSBKLSA-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:30836 )

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	17.3 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

Not Available

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Other Exposures

Source Type	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

C02225

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439681

PDB ID

Not Available

ChEBI ID

30836

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Sajed T, Marcu A, Ramirez M, Pon A, Guo AC, Knox C, Wilson M, Grant JR, Djoumbou Y, Wishart DS: ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res. 2016 Jan 4;44(D1):D495-501. doi: 10.1093/nar/gkv1060. Epub 2015 Oct 19. [PubMed:26481353 ]

Showing metabocard for (2R,3S)-2-Hydroxybutane-1,2,3-tricarboxylate (MMDBc0031739)

MOL for #<Metabolite:0x00005645ca211450>

3D MOL for #<Metabolite:0x00005645ca211450>

3D SDF for #<Metabolite:0x00005645ca211450>

3D-SDF for #<Metabolite:0x00005645ca211450>

PDB for #<Metabolite:0x00005645ca211450>

3D PDB for #<Metabolite:0x00005645ca211450>

SMILES for #<Metabolite:0x00005645ca211450>

INCHI for #<Metabolite:0x00005645ca211450>

Structure for #<Metabolite:0x00005645ca211450>

3D Structure for #<Metabolite:0x00005645ca211450>