MiMeDB: Showing metabocard for 4-Dihydrocyclofarnesine S (MMDBc0023448)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 13:26:52 UTC

Update Date

2025-10-07 16:07:21 UTC

Metabolite ID

MMDBc0023448

Metabolite Identification

Common Name

4-Dihydrocyclofarnesine S

Description

4-Dihydrocyclofarnesine S is a member of the chemical class of cyclofarnesoids, characterized by its unique bicyclic structure. This compound is recognized as a metabolite that plays a role in various biochemical pathways. Notably, it is the most abundant cyclofarnesoid found in young cultures, highlighting its potential significance in plant development and metabolism. The presence of 4-dihydrocyclofarnesine S in these cultures suggests its involvement in the synthesis and regulation of other metabolites, possibly influencing growth and physiological responses. Its structural features may contribute to interactions with biological systems, though specific pathways remain to be fully elucidated. The identification of 4-dihydrocyclofarnesine S as a previously-unknown natural compound underscores the complexity of plant metabolomics and the potential for discovering novel compounds with unique biological roles (PMID:26854131 ). Understanding the chemistry and biological implications of this metabolite could provide insights into its function in plant biology and its potential applications in agriculture or biotechnology.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152115262D          

 21 21  0  0  0  0            999 V2000
    2.8579    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8469    2.8324    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
  8  7  1  0  0  0  0
 10  1  1  0  0  0  0
 10  5  1  0  0  0  0
 10  7  2  0  0  0  0
 11  2  1  0  0  0  0
 12  6  1  0  0  0  0
 12 11  2  0  0  0  0
 13  9  1  0  0  0  0
 13 11  1  0  0  0  0
 14  9  1  0  0  0  0
 15  3  1  0  0  0  0
 15  4  1  0  0  0  0
 15 12  1  0  0  0  0
 15 14  1  0  0  0  0
 16  8  1  0  0  0  0
 17 13  1  0  0  0  0
 18 14  1  0  0  0  0
 19  5  1  0  0  0  0
 20  6  1  0  0  0  0
 21  7  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0023448

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(CO)=C(\C)/C(/[H])=C(\[H])C1=C(C)C(O)CC(O)C1(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C15H24O3/c1-10(7-8-16)5-6-12-11(2)13(17)9-14(18)15(12,3)4/h5-7,13-14,16-18H,8-9H2,1-4H3/b6-5+,10-7+

> <INCHI_KEY>
LGDQPQUPLCETOX-WEYXYWBQSA-N

> <FORMULA>
C15H24O3

> <MOLECULAR_WEIGHT>
252.354

> <EXACT_MASS>
252.172544633

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
29.418265575491738

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-[(1E,3E)-5-hydroxy-3-methylpenta-1,3-dien-1-yl]-4,6,6-trimethylcyclohex-4-ene-1,3-diol

> <ALOGPS_LOGP>
1.69

> <JCHEM_LOGP>
0.8618844146666671

> <ALOGPS_LOGS>
-2.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.923691644498884

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.227014534406585

> <JCHEM_PKA_STRONGEST_BASIC>
-2.1707943293168928

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
75.99159999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.41e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-[(1E,3E)-5-hydroxy-3-methylpenta-1,3-dien-1-yl]-4,6,6-trimethylcyclohex-4-ene-1,3-diol

> <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       5.335   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.324   3.490   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.344   3.490   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       8.002   6.160   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0       3.448   5.287   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       5.335   1.540   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       6.668   2.310   0.000  0.00  0.00           H+0
CONECT    1   10                                                            
CONECT    2   11                                                            
CONECT    3   15                                                            
CONECT    4   15                                                            
CONECT    5    6   10   19                                                  
CONECT    6    5   12   20                                                  
CONECT    7    8   10   21                                                  
CONECT    8    7   16                                                       
CONECT    9   13   14                                                       
CONECT   10    1    5    7                                                  
CONECT   11    2   12   13                                                  
CONECT   12    6   11   15                                                  
CONECT   13    9   11   17                                                  
CONECT   14    9   15   18                                                  
CONECT   15    3    4   12   14                                             
CONECT   16    8                                                            
CONECT   17   13                                                            
CONECT   18   14                                                            
CONECT   19    5                                                            
CONECT   20    6                                                            
CONECT   21    7                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

Synonyms

Not Available

Molecular Formula

C₁₅H₂₄O₃

Average Mass

252.354

Monoisotopic Mass

252.172544633

IUPAC Name

5-[(1E,3E)-5-hydroxy-3-methylpenta-1,3-dien-1-yl]-4,6,6-trimethylcyclohex-4-ene-1,3-diol

Traditional Name

5-[(1E,3E)-5-hydroxy-3-methylpenta-1,3-dien-1-yl]-4,6,6-trimethylcyclohex-4-ene-1,3-diol

CAS Registry Number

Not Available

SMILES

[H]\C(CO)=C(\C)/C(/[H])=C(\[H])C1=C(C)C(O)CC(O)C1(C)C

InChI Identifier

InChI=1S/C15H24O3/c1-10(7-8-16)5-6-12-11(2)13(17)9-14(18)15(12,3)4/h5-7,13-14,16-18H,8-9H2,1-4H3/b6-5+,10-7+

InChI Key

LGDQPQUPLCETOX-WEYXYWBQSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Cyclofarsesane sesquiterpenoid
Sesquiterpenoid
Fatty alcohol
Fatty acyl
Secondary alcohol
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.74 g/L	ALOGPS
logP	1.69	ALOGPS
logP	0.86	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	14.23	ChemAxon
pKa (Strongest Basic)	-2.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	60.69 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	75.99 m³·mol⁻¹	ChemAxon
Polarizability	29.42 Å³	ChemAxon
Number of Rings	1	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_1_2) - 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
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	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

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	Mucoromycota	1	Human feces	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

78436082

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139590777

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 4-Dihydrocyclofarnesine S (MMDBc0023448)

MOL for #<Metabolite:0x00007f8dc8733a90>

3D MOL for #<Metabolite:0x00007f8dc8733a90>

3D SDF for #<Metabolite:0x00007f8dc8733a90>

3D-SDF for #<Metabolite:0x00007f8dc8733a90>

PDB for #<Metabolite:0x00007f8dc8733a90>

3D PDB for #<Metabolite:0x00007f8dc8733a90>

SMILES for #<Metabolite:0x00007f8dc8733a90>

INCHI for #<Metabolite:0x00007f8dc8733a90>

Structure for #<Metabolite:0x00007f8dc8733a90>

3D Structure for #<Metabolite:0x00007f8dc8733a90>