MiMeDB: Showing metabocard for 4-dihydrocyclofarnesine T (MMDBc0023447)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 13:26:49 UTC

Update Date

2022-08-31 06:48:34 UTC

MiMeDB ID

MMDBc0023447

Metabolite Identification

Common Name

4-dihydrocyclofarnesine T

Description

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152115262D          

 19 19  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
    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
    2.1434   -0.4125    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
    2.1434   -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
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  4  2  0  0  0  0
  6  7  1  4  0  0  0
 10  1  1  0  0  0  0
 10  4  1  0  0  0  0
 10  6  2  0  0  0  0
 11  9  1  0  0  0  0
  5 12  1  4  0  0  0
 12 11  2  0  0  0  0
 13  8  1  0  0  0  0
 13 11  1  0  0  0  0
 14  8  1  0  0  0  0
 15  2  1  0  0  0  0
 15  3  1  0  0  0  0
 15 12  1  0  0  0  0
 15 14  1  0  0  0  0
 16  7  1  0  0  0  0
 17  9  1  0  0  0  0
 18 13  1  0  0  0  0
 19 14  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0023447

> <DATABASE_NAME>
MIME

> <SMILES>
CC(=CCO)C=CC1=C(CO)C(O)CC(O)C1(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C15H24O4/c1-10(6-7-16)4-5-12-11(9-17)13(18)8-14(19)15(12,2)3/h4-6,13-14,16-19H,7-9H2,1-3H3

> <INCHI_KEY>
XBAKLQFUYLBTHQ-UHFFFAOYSA-N

> <FORMULA>
C15H24O4

> <MOLECULAR_WEIGHT>
268.353

> <EXACT_MASS>
268.167459253

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
30.004408037658948

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-(5-hydroxy-3-methylpenta-1,3-dien-1-yl)-4-(hydroxymethyl)-6,6-dimethylcyclohex-4-ene-1,3-diol

> <ALOGPS_LOGP>
0.67

> <JCHEM_LOGP>
-0.4188867420000004

> <ALOGPS_LOGS>
-2.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.739360722337516

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.133142949207883

> <JCHEM_PKA_STRONGEST_BASIC>
-2.1707943293177143

> <JCHEM_POLAR_SURFACE_AREA>
80.92

> <JCHEM_REFRACTIVITY>
77.76629999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.50e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-(5-hydroxy-3-methylpenta-1,3-dien-1-yl)-4-(hydroxymethyl)-6,6-dimethylcyclohex-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       2.324   3.490   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.344   3.490   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -0.770   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       4.001  -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  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1   10                                                            
CONECT    2   15                                                            
CONECT    3   15                                                            
CONECT    4    5   10                                                       
CONECT    5    4   12                                                       
CONECT    6    7   10                                                       
CONECT    7    6   16                                                       
CONECT    8   13   14                                                       
CONECT    9   11   17                                                       
CONECT   10    1    4    6                                                  
CONECT   11    9   12   13                                                  
CONECT   12    5   11   15                                                  
CONECT   13    8   11   18                                                  
CONECT   14    8   15   19                                                  
CONECT   15    2    3   12   14                                             
CONECT   16    7                                                            
CONECT   17    9                                                            
CONECT   18   13                                                            
CONECT   19   14                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

Synonyms

Not Available

Chemical Formula

C₁₅H₂₄O₄

Average Molecular Weight

268.353

Monoisotopic Molecular Weight

268.167459253

IUPAC Name

5-(5-hydroxy-3-methylpenta-1,3-dien-1-yl)-4-(hydroxymethyl)-6,6-dimethylcyclohex-4-ene-1,3-diol

Traditional Name

5-(5-hydroxy-3-methylpenta-1,3-dien-1-yl)-4-(hydroxymethyl)-6,6-dimethylcyclohex-4-ene-1,3-diol

CAS Registry Number

Not Available

SMILES

CC(=CCO)C=CC1=C(CO)C(O)CC(O)C1(C)C

InChI Identifier

InChI=1S/C15H24O4/c1-10(6-7-16)4-5-12-11(9-17)13(18)8-14(19)15(12,2)3/h4-6,13-14,16-19H,7-9H2,1-3H3

InChI Key

XBAKLQFUYLBTHQ-UHFFFAOYSA-N

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.95 g/L	ALOGPS
logP	0.67	ALOGPS
logP	-0.42	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	14.13	ChemAxon
pKa (Strongest Basic)	-2.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	80.92 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	77.77 m³·mol⁻¹	ChemAxon
Polarizability	30 Å³	ChemAxon
Number of Rings	1	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 GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		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

Proteins

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Related Health Condition	Evidence Type	Measured in Matrix	Data Source	Reference

Microbial Sources

Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Fungi	Mucoromycota	1	Human Feces	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference	Details

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

Not Available

References

Synthesis Reference

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 T (MMDBc0023447)

MOL for #<Metabolite:0x00007f09200e2060>

3D MOL for #<Metabolite:0x00007f09200e2060>

3D SDF for #<Metabolite:0x00007f09200e2060>

3D-SDF for #<Metabolite:0x00007f09200e2060>

PDB for #<Metabolite:0x00007f09200e2060>

3D PDB for #<Metabolite:0x00007f09200e2060>

SMILES for #<Metabolite:0x00007f09200e2060>

INCHI for #<Metabolite:0x00007f09200e2060>

Structure for #<Metabolite:0x00007f09200e2060>

3D Structure for #<Metabolite:0x00007f09200e2060>