MiMeDB: Showing metabocard for (-)-(R)-cyclo-hydroxysydonic acid (MMDBc0004996)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-14 22:45:50 UTC

Update Date

2025-10-07 16:04:57 UTC

Metabolite ID

MMDBc0004996

Metabolite Identification

Common Name

(-)-(R)-cyclo-hydroxysydonic acid

Description

(-)-(R)-cyclo-hydroxysydonic acid is a cyclopentanoid compound belonging to the class of hydroxylated fatty acids. There is limited literature available on this metabolite, indicating a need for further research to better understand its biological significance and potential applications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152100452D          

 20 21  0  0  1  0            999 V2000
   -1.7925    0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6655    0.3655    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1154    1.8336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3509    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3636    1.4924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0654    1.4924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0780    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.4223   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4905    1.7944    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
  7  4  1  0  0  0  0
  8  4  1  0  0  0  0
 10  5  1  0  0  0  0
 10  9  2  0  0  0  0
 11  6  1  0  0  0  0
 12  9  1  0  0  0  0
 12 11  2  0  0  0  0
 13 10  1  0  0  0  0
 14  1  1  0  0  0  0
 14  2  1  0  0  0  0
 14  7  1  0  0  0  0
 15  3  1  1  0  0  0
 15  8  1  6  0  0  0
 15 11  1  0  0  0  0
 16 13  2  0  0  0  0
 17 13  1  0  0  0  0
 18 14  1  0  0  0  0
 19 12  1  0  0  0  0
 20 15  1  0  0  0  0
 20 19  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0004996

> <DATABASE_NAME>
MIME

> <SMILES>
CC(C)(O)CCC[C@@]1(C)OOC2=C1C=CC(=C2)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H20O5/c1-14(2,18)7-4-8-15(3)11-6-5-10(13(16)17)9-12(11)19-20-15/h5-6,9,18H,4,7-8H2,1-3H3,(H,16,17)/t15-/m1/s1

> <INCHI_KEY>
VPUMRTLIHAHBNQ-OAHLLOKOSA-N

> <FORMULA>
C15H20O5

> <MOLECULAR_WEIGHT>
280.32

> <EXACT_MASS>
280.131073744

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
29.231578347017937

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R)-3-(4-hydroxy-4-methylpentyl)-3-methyl-3H-1,2-benzodioxole-6-carboxylic acid

> <ALOGPS_LOGP>
3.20

> <JCHEM_LOGP>
2.7447721836666665

> <ALOGPS_LOGS>
-3.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.530704522255398

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7568826404885463

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2544111130486923

> <JCHEM_POLAR_SURFACE_AREA>
75.99000000000001

> <JCHEM_REFRACTIVITY>
73.4509

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.46e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-3-(4-hydroxy-4-methylpentyl)-3-methyl-1,2-benzodioxole-6-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0      -3.346   1.246   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.242   0.682   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.949   3.423   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.655   2.016   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.679   2.786   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.989   2.786   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.788  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.012   2.016   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      10.122  -0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       8.788  -2.310   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -2.782   3.350   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       3.322  -0.476   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       2.417   0.770   0.000  0.00  0.00           O+0
CONECT    1   14                                                            
CONECT    2   14                                                            
CONECT    3   15                                                            
CONECT    4    7    8                                                       
CONECT    5    6   10                                                       
CONECT    6    5   11                                                       
CONECT    7    4   14                                                       
CONECT    8    4   15                                                       
CONECT    9   10   12                                                       
CONECT   10    5    9   13                                                  
CONECT   11    6   12   15                                                  
CONECT   12    9   11   19                                                  
CONECT   13   10   16   17                                                  
CONECT   14    1    2    7   18                                             
CONECT   15    3    8   11   20                                             
CONECT   16   13                                                            
CONECT   17   13                                                            
CONECT   18   14                                                            
CONECT   19   12   20                                                       
CONECT   20   15   19                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

Synonyms

Value	Source
(-)-(R)-Cyclo-hydroxysydonate	Generator

Molecular Formula

C₁₅H₂₀O₅

Average Mass

280.32

Monoisotopic Mass

280.131073744

IUPAC Name

(3R)-3-(4-hydroxy-4-methylpentyl)-3-methyl-3H-1,2-benzodioxole-6-carboxylic acid

Traditional Name

(3R)-3-(4-hydroxy-4-methylpentyl)-3-methyl-1,2-benzodioxole-6-carboxylic acid

CAS Registry Number

Not Available

SMILES

CC(C)(O)CCC[C@@]1(C)OOC2=C1C=CC(=C2)C(O)=O

InChI Identifier

InChI=1S/C15H20O5/c1-14(2,18)7-4-8-15(3)11-6-5-10(13(16)17)9-12(11)19-20-15/h5-6,9,18H,4,7-8H2,1-3H3,(H,16,17)/t15-/m1/s1

InChI Key

VPUMRTLIHAHBNQ-OAHLLOKOSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzenoids. These are aromatic compounds containing one or more benzene rings.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Not Available

Sub Class

Not Available

Direct Parent

Benzenoids

Alternative Parents

Substituents

Benzenoid
Tertiary alcohol
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.15 g/L	ALOGPS
logP	3.2	ALOGPS
logP	2.74	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	3.76	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.99 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	73.45 m³·mol⁻¹	ChemAxon
Polarizability	29.23 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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 (TMS_2_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	178.8
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (void)	2025-10-23	32.3
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	433.2
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	609.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	596.4
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-23	290.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	2090.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	73.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	337.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	441.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	358.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	176.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	165.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (void)	2025-10-23	14.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	297.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	130.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	391.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1277.9
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	982.7

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	(-)-(R)-cyclo-hydroxysydonic acid_TMS_1	CC(C)(CCC[C@@]1(C)OOC2=CC(C(=O)O)=CC=C21)O[Si](C)(C)C	standard non polar	2025-10-23	1931.57
Gas Chromatography	(-)-(R)-cyclo-hydroxysydonic acid_TMS_2	CC(C)(O)CCC[C@@]1(C)OOC2=CC(C(=O)O[Si](C)(C)C)=CC=C21	standard non polar	2025-10-23	1859.48
Gas Chromatography	(-)-(R)-cyclo-hydroxysydonic acid_TMS_3	CC(C)(CCC[C@@]1(C)OOC2=CC(C(=O)O[Si](C)(C)C)=CC=C21)O[Si](C)(C)C	standard non polar	2025-10-23	2037.64
Gas Chromatography	(-)-(R)-cyclo-hydroxysydonic acid_TMS_1	CC(C)(CCC[C@@]1(C)OOC2=CC(C(=O)O)=CC=C21)O[Si](C)(C)C	standard polar	2025-10-23	2645.87
Gas Chromatography	(-)-(R)-cyclo-hydroxysydonic acid_TMS_2	CC(C)(O)CCC[C@@]1(C)OOC2=CC(C(=O)O[Si](C)(C)C)=CC=C21	standard polar	2025-10-23	1654.04
Gas Chromatography	(-)-(R)-cyclo-hydroxysydonic acid_TMS_3	CC(C)(CCC[C@@]1(C)OOC2=CC(C(=O)O[Si](C)(C)C)=CC=C21)O[Si](C)(C)C	standard polar	2025-10-23	1883.16

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

Not Available

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

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	2	Human feces; Human sputum; Human	Metabolic reconstruction

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

78440857

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139584285

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for (-)-(R)-cyclo-hydroxysydonic acid (MMDBc0004996)

MOL for #<Metabolite:0x00007f9ac72d9ad8>

3D MOL for #<Metabolite:0x00007f9ac72d9ad8>

3D SDF for #<Metabolite:0x00007f9ac72d9ad8>

3D-SDF for #<Metabolite:0x00007f9ac72d9ad8>

PDB for #<Metabolite:0x00007f9ac72d9ad8>

3D PDB for #<Metabolite:0x00007f9ac72d9ad8>

SMILES for #<Metabolite:0x00007f9ac72d9ad8>

INCHI for #<Metabolite:0x00007f9ac72d9ad8>

Structure for #<Metabolite:0x00007f9ac72d9ad8>

3D Structure for #<Metabolite:0x00007f9ac72d9ad8>