Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 02:42:20 UTC

Update Date

2022-03-07 02:56:52 UTC

HMDB ID

HMDB0041060

Secondary Accession Numbers

HMDB41060

Metabolite Identification

Common Name

Dehydro-4-methoxycyclobrassinin

Description

Dehydro-4-methoxycyclobrassinin belongs to the class of organic compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole. Dehydro-4-methoxycyclobrassinin has been detected, but not quantified in, brassicas and root vegetables. This could make dehydro-4-methoxycyclobrassinin a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Dehydro-4-methoxycyclobrassinin.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

  Mrv0541 05061312212D          

 17 19  0  0  0  0            999 V2000
    3.1956   -1.7698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4515    0.1425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9604    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4084    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7054   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9694   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5214    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6014    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8985   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3464    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2665    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0925    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1624   -0.2006    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339    1.5105    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6435   -1.1567    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8995    0.7556    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.4595    1.1971    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  5  3  1  0  0  0  0
  7  6  2  0  0  0  0
  8  4  1  0  0  0  0
  9  5  2  0  0  0  0
 10  7  1  0  0  0  0
 10  8  2  0  0  0  0
 10  9  1  0  0  0  0
 11  7  1  0  0  0  0
 13  6  1  0  0  0  0
 13 12  2  0  0  0  0
 14  8  1  0  0  0  0
 14 11  2  0  0  0  0
 15  1  1  0  0  0  0
 15  9  1  0  0  0  0
 16  2  1  0  0  0  0
 16 12  1  0  0  0  0
 17 11  1  0  0  0  0
 17 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0041060

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=CC=CC2=C1C1=CN=C(SC)SC1=N2

> <INCHI_IDENTIFIER>
InChI=1S/C12H10N2OS2/c1-15-9-5-3-4-8-10(9)7-6-13-12(16-2)17-11(7)14-8/h3-6H,1-2H3

> <INCHI_KEY>
JDYSKRAQSOYTDY-UHFFFAOYSA-N

> <FORMULA>
C12H10N2OS2

> <MOLECULAR_WEIGHT>
262.351

> <EXACT_MASS>
262.023454332

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
27.354586719866944

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-methoxy-2-(methylsulfanyl)-[1,3]thiazino[6,5-b]indole

> <ALOGPS_LOGP>
2.49

> <JCHEM_LOGP>
3.407534027666667

> <ALOGPS_LOGS>
-3.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
3.6064750898490043

> <JCHEM_POLAR_SURFACE_AREA>
35.010000000000005

> <JCHEM_REFRACTIVITY>
70.07

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.34e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-methoxy-2-(methylsulfanyl)-[1,3]thiazino[6,5-b]indole

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       5.965  -3.304   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.709   0.266   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.393   1.090   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.362   2.235   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.917  -0.374   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.810  -0.695   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.840   0.450   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.856   1.914   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.411  -0.695   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.380   0.450   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.364   1.914   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.173   1.090   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       0.303  -0.374   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       3.610   2.820   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0       4.935  -2.159   0.000  0.00  0.00           O+0
HETATM   16  S   UNK     0      -1.679   1.410   0.000  0.00  0.00           S+0
HETATM   17  S   UNK     0       0.858   2.235   0.000  0.00  0.00           S+0
CONECT    1   15                                                            
CONECT    2   16                                                            
CONECT    3    4    5                                                       
CONECT    4    3    8                                                       
CONECT    5    3    9                                                       
CONECT    6    7   13                                                       
CONECT    7    6   10   11                                                  
CONECT    8    4   10   14                                                  
CONECT    9    5   10   15                                                  
CONECT   10    7    8    9                                                  
CONECT   11    7   14   17                                                  
CONECT   12   13   16   17                                                  
CONECT   13    6   12                                                       
CONECT   14    8   11                                                       
CONECT   15    1    9                                                       
CONECT   16    2   12                                                       
CONECT   17   11   12                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

COMPND    HMDB0041060
HETATM    1  C1  UNL     1      -3.442  -2.116   0.253  1.00  0.00           C  
HETATM    2  O1  UNL     1      -2.286  -1.346   0.178  1.00  0.00           O  
HETATM    3  C2  UNL     1      -2.238   0.016  -0.025  1.00  0.00           C  
HETATM    4  C3  UNL     1      -3.403   0.777  -0.180  1.00  0.00           C  
HETATM    5  C4  UNL     1      -3.302   2.137  -0.380  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.038   2.716  -0.423  1.00  0.00           C  
HETATM    7  C6  UNL     1      -0.888   1.970  -0.271  1.00  0.00           C  
HETATM    8  N1  UNL     1       0.422   2.285  -0.272  1.00  0.00           N  
HETATM    9  C7  UNL     1       1.182   1.210  -0.084  1.00  0.00           C  
HETATM   10  S1  UNL     1       2.845   0.784   0.038  1.00  0.00           S  
HETATM   11  C8  UNL     1       3.099  -0.882   0.297  1.00  0.00           C  
HETATM   12  S2  UNL     1       4.678  -1.692   0.474  1.00  0.00           S  
HETATM   13  C9  UNL     1       6.046  -0.517   0.345  1.00  0.00           C  
HETATM   14  N2  UNL     1       1.996  -1.617   0.368  1.00  0.00           N  
HETATM   15  C10 UNL     1       0.743  -1.216   0.265  1.00  0.00           C  
HETATM   16  C11 UNL     1       0.292   0.060   0.057  1.00  0.00           C  
HETATM   17  C12 UNL     1      -0.991   0.609  -0.070  1.00  0.00           C  
HETATM   18  H1  UNL     1      -3.189  -3.029   0.867  1.00  0.00           H  
HETATM   19  H2  UNL     1      -4.254  -1.610   0.784  1.00  0.00           H  
HETATM   20  H3  UNL     1      -3.725  -2.434  -0.781  1.00  0.00           H  
HETATM   21  H4  UNL     1      -4.350   0.259  -0.135  1.00  0.00           H  
HETATM   22  H5  UNL     1      -4.212   2.721  -0.500  1.00  0.00           H  
HETATM   23  H6  UNL     1      -2.008   3.785  -0.583  1.00  0.00           H  
HETATM   24  H7  UNL     1       5.702   0.476  -0.042  1.00  0.00           H  
HETATM   25  H8  UNL     1       6.808  -0.984  -0.319  1.00  0.00           H  
HETATM   26  H9  UNL     1       6.558  -0.381   1.339  1.00  0.00           H  
HETATM   27  H10 UNL     1      -0.046  -1.982   0.352  1.00  0.00           H  
CONECT    1    2   18   19   20
CONECT    2    3
CONECT    3    4    4   17
CONECT    4    5   21
CONECT    5    6    6   22
CONECT    6    7   23
CONECT    7    8   17   17
CONECT    8    9    9
CONECT    9   10   16
CONECT   10   11
CONECT   11   12   14   14
CONECT   12   13
CONECT   13   24   25   26
CONECT   14   15
CONECT   15   16   16   27
CONECT   16   17
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
5-Methoxy-2-(methylsulphanyl)-[1,3]thiazino[6,5-b]indole	HMDB

Chemical Formula

C₁₂H₁₀N₂OS₂

Average Molecular Weight

262.351

Monoisotopic Molecular Weight

262.023454332

IUPAC Name

5-methoxy-2-(methylsulfanyl)-[1,3]thiazino[6,5-b]indole

Traditional Name

5-methoxy-2-(methylsulfanyl)-[1,3]thiazino[6,5-b]indole

CAS Registry Number

154933-74-1

SMILES

COC1=CC=CC2=C1C1=CN=C(SC)SC1=N2

InChI Identifier

InChI=1S/C12H10N2OS2/c1-15-9-5-3-4-8-10(9)7-6-13-12(16-2)17-11(7)14-8/h3-6H,1-2H3

InChI Key

JDYSKRAQSOYTDY-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

Indoles

Alternative Parents

Substituents

Indole
Aryl thioether
Anisole
Alkyl aryl ether
Alkylarylthioether
Benzenoid
Heteroaromatic compound
Pyrrole
Ether
Azacycle
Sulfenyl compound
Thioether
Organic nitrogen compound
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0041060)
Cytoplasm (HMDB: HMDB0041060)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0041060)

Source

Exogenous

Exogenous (HMDB: HMDB0041060)

Food

Food (HMDB: HMDB0041060)

Vegetable

Brassica

Brassicas (FooDB: FOOD00857)

Root vegetable

Root vegetables (FooDB: FOOD00873)

Endogenous

Plant

Plant (HMDB: HMDB0041060)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0041060)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	142 - 143 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.073 g/L	ALOGPS
logP	2.49	ALOGPS
logP	3.41	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Basic)	3.61	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	35.01 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	70.07 m³·mol⁻¹	ChemAxon
Polarizability	27.35 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	156.171	31661259
DarkChem	[M-H]-	158.863	31661259
DeepCCS	[M+H]+	148.492	30932474
DeepCCS	[M-H]-	146.134	30932474
DeepCCS	[M-2H]-	180.559	30932474
DeepCCS	[M+Na]+	155.46	30932474
AllCCS	[M+H]+	155.6	32859911
AllCCS	[M+H-H2O]+	151.9	32859911
AllCCS	[M+NH4]+	159.0	32859911
AllCCS	[M+Na]+	160.0	32859911
AllCCS	[M-H]-	158.1	32859911
AllCCS	[M+Na-2H]-	157.7	32859911
AllCCS	[M+HCOO]-	157.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Dehydro-4-methoxycyclobrassinin	COC1=CC=CC2=C1C1=CN=C(SC)SC1=N2	3416.3	Standard polar	33892256
Dehydro-4-methoxycyclobrassinin	COC1=CC=CC2=C1C1=CN=C(SC)SC1=N2	2457.4	Standard non polar	33892256
Dehydro-4-methoxycyclobrassinin	COC1=CC=CC2=C1C1=CN=C(SC)SC1=N2	2537.2	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Dehydro-4-methoxycyclobrassinin GC-MS (Non-derivatized) - 70eV, Positive	splash10-006t-1960000000-0a0ae368d89cb5604236	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dehydro-4-methoxycyclobrassinin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dehydro-4-methoxycyclobrassinin 10V, Positive-QTOF	splash10-03di-1190000000-4ff2d12de800d5cc38f5	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dehydro-4-methoxycyclobrassinin 20V, Positive-QTOF	splash10-03xr-1090000000-170ac3a6c0603a80f54f	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dehydro-4-methoxycyclobrassinin 40V, Positive-QTOF	splash10-00ba-2910000000-461aaa000d3cba7ef835	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dehydro-4-methoxycyclobrassinin 10V, Negative-QTOF	splash10-03xs-2090000000-2af6405a4f7705ed8600	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dehydro-4-methoxycyclobrassinin 20V, Negative-QTOF	splash10-01ba-9080000000-b317696a19613bb4f630	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dehydro-4-methoxycyclobrassinin 40V, Negative-QTOF	splash10-0a4i-9320000000-0e9c65965ca3b10e920e	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dehydro-4-methoxycyclobrassinin 10V, Negative-QTOF	splash10-03di-0090000000-ebeed3751c7ccd8b58a2	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dehydro-4-methoxycyclobrassinin 20V, Negative-QTOF	splash10-03di-0090000000-ebeed3751c7ccd8b58a2	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dehydro-4-methoxycyclobrassinin 40V, Negative-QTOF	splash10-0bti-0980000000-38d9f889fdb0ec3159d6	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dehydro-4-methoxycyclobrassinin 10V, Positive-QTOF	splash10-03di-0090000000-b5d742068d8cb3630b7e	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dehydro-4-methoxycyclobrassinin 20V, Positive-QTOF	splash10-03di-0090000000-b5d742068d8cb3630b7e	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dehydro-4-methoxycyclobrassinin 40V, Positive-QTOF	splash10-05o0-0290000000-9c7c393b110f6b233b4b	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB020934

KNApSAcK ID

C00055332

Chemspider ID

8508391

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10332932

PDB ID

Not Available

ChEBI ID

169362

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Dehydro-4-methoxycyclobrassinin (HMDB0041060)

MOL for HMDB0041060 (Dehydro-4-methoxycyclobrassinin)

3D MOL for HMDB0041060 (Dehydro-4-methoxycyclobrassinin)

3D SDF for HMDB0041060 (Dehydro-4-methoxycyclobrassinin)

3D-SDF for HMDB0041060 (Dehydro-4-methoxycyclobrassinin)

PDB for HMDB0041060 (Dehydro-4-methoxycyclobrassinin)

3D PDB for HMDB0041060 (Dehydro-4-methoxycyclobrassinin)

SMILES for HMDB0041060 (Dehydro-4-methoxycyclobrassinin)

INCHI for HMDB0041060 (Dehydro-4-methoxycyclobrassinin)

Structure for HMDB0041060 (Dehydro-4-methoxycyclobrassinin)

3D Structure for HMDB0041060 (Dehydro-4-methoxycyclobrassinin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra