MiMeDB: Showing metabocard for (1R,2S)-homoisocitrate (MMDBc0047867)

Microbial

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 15:46:41 UTC

Update Date

2025-10-07 16:08:07 UTC

Metabolite ID

MMDBc0047867

Metabolite Identification

Common Name

(1R,2S)-homoisocitrate

Description

(1R,2S)-homoisocitrate is a dicarboxylic acid and a member of the citric acid cycle intermediates. There is limited literature available on this metabolite, indicating that it may not be extensively studied in the context of biochemical pathways or clinical relevance.

Structure

MOL SDF PDB SMILES InChI


  Mrv1572012201517002D          

 16 15  0  0  0  0            999 V2000
   -0.3572    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7861    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717    0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3572   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7861    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5006    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7861    1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.0717    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572   -1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.5006    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7861   -0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.3572    0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717   -0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  3  6  1  6  0  0  0
  7  5  1  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
  5 10  1  6  0  0  0
 11  6  2  0  0  0  0
 12  6  1  0  0  0  0
 13  7  2  0  0  0  0
 14  7  1  0  0  0  0
  3 15  1  6  0  0  0
  5 16  1  6  0  0  0
M  CHG  3   9  -1  12  -1  14  -1
M  END
> <DATABASE_ID>
MMDBc0047867

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](O)(C([O-])=O)[C@]([H])(CCC([O-])=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H10O7/c8-4(9)2-1-3(6(11)12)5(10)7(13)14/h3,5,10H,1-2H2,(H,8,9)(H,11,12)(H,13,14)/p-3/t3-,5+/m0/s1

> <INCHI_KEY>
OEJZZCGRGVFWHK-WVZVXSGGSA-K

> <FORMULA>
C7H7O7

> <MOLECULAR_WEIGHT>
203.128

> <EXACT_MASS>
203.020823305

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
16.341093524533

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate

> <ALOGPS_LOGP>
-0.53

> <JCHEM_LOGP>
-1.0017595846666665

> <ALOGPS_LOGS>
-0.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.9340746844137886

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.120282696000762

> <JCHEM_PKA_STRONGEST_BASIC>
-4.012518164144468

> <JCHEM_POLAR_SURFACE_AREA>
140.62

> <JCHEM_REFRACTIVITY>
72.8284

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.05e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(-)-homoisocitrate(3-)

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-DEC-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-DEC-15         0                                  
HETATM    1  C   UNK     0      -0.667   0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.001   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.334   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.001   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.667  -1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.334   0.000   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -4.668   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -3.334   2.310   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0       2.001   2.310   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       2.001  -2.310   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -0.667  -2.310   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0       4.668   0.770   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       3.334  -1.540   0.000  0.00  0.00           O-1
HETATM   15  H   UNK     0       0.667   1.540   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       2.001  -0.770   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5    6   15                                             
CONECT    4    2    8    9                                                  
CONECT    5    3    7   10   16                                             
CONECT    6    3   11   12                                                  
CONECT    7    5   13   14                                                  
CONECT    8    4                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    6                                                            
CONECT   12    6                                                            
CONECT   13    7                                                            
CONECT   14    7                                                            
CONECT   15    3                                                            
CONECT   16    5                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

Synonyms

Value	Source
(-)-1-Hydroxy-1,2,4-butanetricarboxylate	ChEBI
(1R,2S)-1-Hydroxybutane-1,2,4-tricarboxylate	ChEBI
(-)-1-Hydroxy-1,2,4-butanetricarboxylic acid	Generator
(1R,2S)-1-Hydroxybutane-1,2,4-tricarboxylic acid	Generator
(1R,2S)-Homoisocitric acid	Generator
(1R,2S)-Homoisocitrate	ChEBI
(-)-Homoisocitric acid(3-)	Generator

Molecular Formula

C₇H₇O₇

Average Mass

203.128

Monoisotopic Mass

203.020823305

IUPAC Name

(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate

Traditional Name

(-)-homoisocitrate(3-)

CAS Registry Number

Not Available

SMILES

[H][C@](O)(C([O-])=O)[C@]([H])(CCC([O-])=O)C([O-])=O

InChI Identifier

InChI=1S/C7H10O7/c8-4(9)2-1-3(6(11)12)5(10)7(13)14/h3,5,10H,1-2H2,(H,8,9)(H,11,12)(H,13,14)/p-3/t3-,5+/m0/s1

InChI Key

OEJZZCGRGVFWHK-WVZVXSGGSA-K

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
Beta-hydroxy acid
Monosaccharide
Hydroxy acid
Secondary alcohol
Carboxylic acid
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

homoisocitrate(3-) (CHEBI:15404 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	90.5 g/L	ALOGPS
logP	-0.53	ALOGPS
logP	-1	ChemAxon
logS	-0.45	ALOGPS
pKa (Strongest Acidic)	3.12	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	140.62 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	72.83 m³·mol⁻¹	ChemAxon
Polarizability	16.34 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 LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0490000000-dd746e5732374387d6d1	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-002b-1910000000-9bdd06d800a83af17f1b	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00mk-5900000000-64c8415d0e8f4960d589	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0190000000-752ee9d3f49874d330f2	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-2490000000-c6c07e91d309c216c375	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-016r-9600000000-4a38a60480350fa7ac6e	2016-09-14	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

Microbial Pathways

Pathways

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0019591	cis-homoaconitate	(1R,2S)-homoisocitrate	Homoaconitase, mitochondrial	Hydrolysis	PathBank	31602464
MMDBr0019592	(1R,2S)-homoisocitrate	Oxoadipic acid	Homoisocitrate dehydrogenase, mitochondrial	Dehydrogenation	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
Eukaryota/Fungi	Ascomycota	17	Human feces; Human saliva	Unknown
Archaea/Archaea	Euryarchaeota	5
Bacteria/Eubacteria	Deinococcus-thermus	2
Eukaryota/Fungi	Basidiomycota	3

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5459812

PDB ID

Not Available

ChEBI ID

15404

CMMC Knowledgebase

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
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 (1R,2S)-homoisocitrate (MMDBc0047867)

MOL for #<Metabolite:0x00007fd4490c5b00>

3D MOL for #<Metabolite:0x00007fd4490c5b00>

3D SDF for #<Metabolite:0x00007fd4490c5b00>

3D-SDF for #<Metabolite:0x00007fd4490c5b00>

PDB for #<Metabolite:0x00007fd4490c5b00>

3D PDB for #<Metabolite:0x00007fd4490c5b00>

SMILES for #<Metabolite:0x00007fd4490c5b00>

INCHI for #<Metabolite:0x00007fd4490c5b00>

Structure for #<Metabolite:0x00007fd4490c5b00>

3D Structure for #<Metabolite:0x00007fd4490c5b00>