MiMeDB: Showing metabocard for (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylic acid (MMDBc0033019)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:31:21 UTC

Update Date

2025-01-15 20:10:20 UTC

Metabolite ID

MMDBc0033019

Metabolite Identification

Common Name

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

Description

myo-Inositol 1,3,4,5,6-pentakisphosphate, also known as Ins(1,3,4,5,6)P5 or inositol pentaphosphate, is an inositol polyphosphate of emerging significance in cellular signalling. Both Ins(1,3,4,5,6)P5 and its C-2 epimer scyllo-inositol pentakisphosphate (scyllo-InsP(5)) were synthesized from the same myo-inositol-based precursor (PMID: 16755629 ). InsP6, Ins(1,3,4,5,6)P5, and their close metabolic relatives are amongst the more abundant intracellular inositol polyphosphates. They are involved in chromatin organization, DNA maintenance, gene transcription, nuclear mRNA transport, membrane trafficking, and control of cell proliferation (PMID: 14992690 ).

Structure

MOL SDF PDB SMILES InChI

ChEBI
  Mrv0541 02241222242D          

 14 13  0  0  1  0            999 V2000
    5.8153   -3.4765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5352   -3.8795    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.2408   -3.4765    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.9606   -3.8795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0955   -3.8795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3756   -3.4621    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0955   -4.7002    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5352   -4.7146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8153   -5.1178    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2408   -5.1178    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2408   -2.6414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9606   -2.2382    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5352   -2.2382    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9606   -3.0588    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  5  1  1  0  0  0  0
  3  2  1  0  0  0  0
  8  2  1  0  0  0  0
  4  3  1  0  0  0  0
 11  3  1  0  0  0  0
  3 14  1  6  0  0  0
  6  5  2  0  0  0  0
  7  5  1  0  0  0  0
  9  8  2  0  0  0  0
 10  8  1  0  0  0  0
 12 11  2  0  0  0  0
 13 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033019

> <DATABASE_NAME>
MIME

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

> <INCHI_KEY>
HHKPKXCSHMJWCF-WVBDSBKLSA-N

> <FORMULA>
C7H10O7

> <MOLECULAR_WEIGHT>
206.1501

> <EXACT_MASS>
206.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
17.258105682756803

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S)-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>
4.805179537739236

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1668703375685876

> <JCHEM_PKA_STRONGEST_BASIC>
-4.066922204255973

> <JCHEM_POLAR_SURFACE_AREA>
132.13

> <JCHEM_REFRACTIVITY>
40.4294

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.49e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylisocitrate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: ChEBI                                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      10.855  -6.489   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.199  -7.242   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.516  -6.489   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.860  -7.242   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.512  -7.242   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       8.168  -6.463   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       9.512  -8.774   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      12.199  -8.801   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      10.855  -9.553   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      13.516  -9.553   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      13.516  -4.931   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      14.860  -4.178   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      12.199  -4.178   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      14.860  -5.710   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3    8                                                  
CONECT    3    2    4   11   14                                             
CONECT    4    3                                                            
CONECT    5    1    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    2    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    3   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    3                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Synonyms

Value	Source
(2S,3R)-3-Hydroxybutane-1,2,3-tricarboxylate	ChEBI
3-Carboxy-2,3-dideoxy-4-C-methyl-L-threo-pentaric acid	ChEBI
Methylisocitric acid	ChEBI
Methylisocitrate	Kegg
(2S,3R)-3-Hydroxybutane-1,2,3-tricarboxylic acid	Generator
3-Carboxy-2,3-dideoxy-4-C-methyl-L-threo-pentarate	Generator
a-Methylisocitrate	Generator
a-Methylisocitric acid	Generator
alpha-Methylisocitrate	Generator
Α-methylisocitrate	Generator
Α-methylisocitric acid	Generator

Molecular Formula

C₇H₁₀O₇

Average Mass

206.1501

Monoisotopic Mass

206.042652674

IUPAC Name

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

Traditional Name

methylisocitrate

CAS Registry Number

20298-95-7

SMILES

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

InChI Key

HHKPKXCSHMJWCF-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

tricarboxylic acid (CHEBI:15607 )
methylisocitric acid (CHEBI:15607 )

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	17.26 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

Cytoplasm
Nucleus

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
Eukaryota/Fungi	Ascomycota	22	Human feces; Human saliva; Human supragingival plaque	Unknown
Eukaryota/Fungi	Basidiomycota	2	Human feces
Bacteria	Actinobacteria	1	Human
Bacteria/Eubacteria	Actinobacteria	8	Human
Archaea/Archaea	Crenarchaeota	1
Bacteria	Proteobacteria	2	Human ; Human feces
Bacteria/Eubacteria	Proteobacteria	14	Human ; Human feces
Bacteria/Eubacteria	Deinococcus-thermus	2
Bacteria/Eubacteria	Firmicutes	9	Human ; Human feces
Bacteria	nah	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

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

DB04072

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C04593

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5459784

PDB ID

Not Available

ChEBI ID

15607

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Barker CJ, Wright J, Hughes PJ, Kirk CJ, Michell RH: Complex changes in cellular inositol phosphate complement accompany transit through the cell cycle. Biochem J. 2004 Jun 1;380(Pt 2):465-73. doi: 10.1042/BJ20031872. [PubMed:14992690 ]
Riley AM, Trusselle M, Kuad P, Borkovec M, Cho J, Choi JH, Qian X, Shears SB, Spiess B, Potter BV: scyllo-inositol pentakisphosphate as an analogue of myo-inositol 1,3,4,5,6-pentakisphosphate: chemical synthesis, physicochemistry and biological applications. Chembiochem. 2006 Jul;7(7):1114-22. doi: 10.1002/cbic.200600037. [PubMed:16755629 ]

Showing metabocard for (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylic acid (MMDBc0033019)

MOL for #<Metabolite:0x00007f921db650b0>

3D MOL for #<Metabolite:0x00007f921db650b0>

3D SDF for #<Metabolite:0x00007f921db650b0>

3D-SDF for #<Metabolite:0x00007f921db650b0>

PDB for #<Metabolite:0x00007f921db650b0>

3D PDB for #<Metabolite:0x00007f921db650b0>

SMILES for #<Metabolite:0x00007f921db650b0>

INCHI for #<Metabolite:0x00007f921db650b0>

Structure for #<Metabolite:0x00007f921db650b0>

3D Structure for #<Metabolite:0x00007f921db650b0>