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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 21:01:55 UTC

Update Date

2022-03-07 02:54:43 UTC

HMDB ID

HMDB0035974

Secondary Accession Numbers

HMDB35974

Metabolite Identification

Common Name

(S)-Spirobrassinin

Description

(S)-Spirobrassinin belongs to the class of organic compounds known as indolines. Indolines are compounds containing an indole moiety, which consists of pyrrolidine ring fused to benzene to form 2,3-dihydroindole (S)-Spirobrassinin has been detected, but not quantified in, a few different foods, such as cauliflowers (Brassica oleracea var. botrytis), chinese cabbages (Brassica rapa), and radishes (Raphanus sativus). This could make (S)-spirobrassinin a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on (S)-Spirobrassinin.

Structure

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


  Mrv0541 02241208332D          

 16 18  0  0  0  0            999 V2000
   -1.7324   -1.6502    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9072   -1.4850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4117   -2.1450    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3296   -1.8145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0725   -2.1450    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7324   -1.6502    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6502   -0.8251    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8252   -0.4955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1644   -0.9895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5768   -0.7420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3198   -0.3303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3198    0.4948    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5768    0.7421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3295    1.4851    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8251    2.1450    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1643    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2 10  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  9  2  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 16  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 13 16  1  0  0  0  0
 14 15  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0035974

> <DATABASE_NAME>
hmdb

> <SMILES>
CSC1=NCC2(S1)C(=O)NC1=C2C=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C11H10N2OS2/c1-15-10-12-6-11(16-10)7-4-2-3-5-8(7)13-9(11)14/h2-5H,6H2,1H3,(H,13,14)

> <INCHI_KEY>
FUHQSEOSBHASCH-UHFFFAOYSA-N

> <FORMULA>
C11H10N2OS2

> <MOLECULAR_WEIGHT>
250.34

> <EXACT_MASS>
250.023454332

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
25.265382716269187

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5'-(methylsulfanyl)-1,2-dihydro-3'H-spiro[indole-3,2'-[1,4]thiazole]-2-one

> <ALOGPS_LOGP>
2.05

> <JCHEM_LOGP>
2.756003960666667

> <ALOGPS_LOGS>
-2.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.53392071518364

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.645687658516614

> <JCHEM_PKA_STRONGEST_BASIC>
3.0353252510691675

> <JCHEM_POLAR_SURFACE_AREA>
41.46

> <JCHEM_REFRACTIVITY>
69.3867

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.29e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5'-(methylsulfanyl)-1H,3'H-spiro[indole-3,2'-[1,4]thiazole]-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0      -3.234  -3.080   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.693  -2.772   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -0.769  -4.004   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       0.615  -3.387   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.002  -4.004   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.234  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.080  -1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.540  -0.925   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.307  -1.847   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.077  -1.385   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.464  -0.617   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -2.464   0.924   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      -1.077   1.385   0.000  0.00  0.00           C+0
HETATM   14  S   UNK     0      -0.615   2.772   0.000  0.00  0.00           S+0
HETATM   15  C   UNK     0      -1.540   4.004   0.000  0.00  0.00           C+0
HETATM   16  S   UNK     0      -0.307   0.000   0.000  0.00  0.00           S+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    4    8   10                                                  
CONECT   10    2    9   11   16                                             
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   10   13                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   36    0
END

COMPND    HMDB0035974
HETATM    1  C1  UNL     1      -4.961   0.175  -0.315  1.00  0.00           C  
HETATM    2  S1  UNL     1      -3.889  -0.173   1.103  1.00  0.00           S  
HETATM    3  C2  UNL     1      -2.289  -0.651   0.499  1.00  0.00           C  
HETATM    4  N1  UNL     1      -1.919  -0.740  -0.688  1.00  0.00           N  
HETATM    5  C3  UNL     1      -0.634  -1.127  -1.009  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.317  -1.021   0.137  1.00  0.00           C  
HETATM    7  S2  UNL     1      -0.886  -1.093   1.509  1.00  0.00           S  
HETATM    8  C5  UNL     1       1.230  -2.152   0.132  1.00  0.00           C  
HETATM    9  O1  UNL     1       0.910  -3.361   0.116  1.00  0.00           O  
HETATM   10  N2  UNL     1       2.550  -1.626   0.147  1.00  0.00           N  
HETATM   11  C6  UNL     1       2.452  -0.208   0.162  1.00  0.00           C  
HETATM   12  C7  UNL     1       3.434   0.790   0.180  1.00  0.00           C  
HETATM   13  C8  UNL     1       3.123   2.130   0.192  1.00  0.00           C  
HETATM   14  C9  UNL     1       1.789   2.477   0.185  1.00  0.00           C  
HETATM   15  C10 UNL     1       0.794   1.524   0.168  1.00  0.00           C  
HETATM   16  C11 UNL     1       1.129   0.182   0.156  1.00  0.00           C  
HETATM   17  H1  UNL     1      -6.035   0.055  -0.068  1.00  0.00           H  
HETATM   18  H2  UNL     1      -4.801   1.245  -0.639  1.00  0.00           H  
HETATM   19  H3  UNL     1      -4.656  -0.511  -1.131  1.00  0.00           H  
HETATM   20  H4  UNL     1      -0.248  -0.404  -1.789  1.00  0.00           H  
HETATM   21  H5  UNL     1      -0.538  -2.124  -1.499  1.00  0.00           H  
HETATM   22  H6  UNL     1       3.465  -2.167   0.148  1.00  0.00           H  
HETATM   23  H7  UNL     1       4.445   0.467   0.184  1.00  0.00           H  
HETATM   24  H8  UNL     1       3.897   2.902   0.206  1.00  0.00           H  
HETATM   25  H9  UNL     1       1.567   3.548   0.195  1.00  0.00           H  
HETATM   26  H10 UNL     1      -0.246   1.865   0.163  1.00  0.00           H  
CONECT    1    2   17   18   19
CONECT    2    3
CONECT    3    4    4    7
CONECT    4    5
CONECT    5    6   20   21
CONECT    6    7    8   16
CONECT    8    9    9   10
CONECT   10   11   22
CONECT   11   12   12   16
CONECT   12   13   23
CONECT   13   14   14   24
CONECT   14   15   25
CONECT   15   16   16   26
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
5'-(Methylsulphanyl)-3'H-spiro[indole-3,2'-[1,4]thiazole]-2-ol	Generator

Chemical Formula

C₁₁H₁₀N₂OS₂

Average Molecular Weight

250.34

Monoisotopic Molecular Weight

250.023454332

IUPAC Name

5'-(methylsulfanyl)-1,2-dihydro-3'H-spiro[indole-3,2'-[1,4]thiazole]-2-one

Traditional Name

5'-(methylsulfanyl)-1H,3'H-spiro[indole-3,2'-[1,4]thiazole]-2-one

CAS Registry Number

Not Available

SMILES

CSC1=NCC2(S1)C(=O)NC1=C2C=CC=C1

InChI Identifier

InChI=1S/C11H10N2OS2/c1-15-10-12-6-11(16-10)7-4-2-3-5-8(7)13-9(11)14/h2-5H,6H2,1H3,(H,13,14)

InChI Key

FUHQSEOSBHASCH-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indolines. Indolines are compounds containing an indole moiety, which consists of pyrrolidine ring fused to benzene to form 2,3-dihydroindole.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indolines

Direct Parent

Indolines

Alternative Parents

Substituents

Dihydroindole
Benzenoid
Meta-thiazoline
Carboxamide group
Lactam
Secondary carboxylic acid amide
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Sulfenyl compound
Carboxylic acid derivative
Azacycle
Organopnictogen compound
Organic oxygen compound
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0035974)
Cytoplasm (HMDB: HMDB0035974)

Source

Exogenous

Exogenous (HMDB: HMDB0035974)

Food

Vegetable

Brassica

Brassicas (FooDB: FOOD00857)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	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	0.43 g/L	ALOGPS
logP	2.05	ALOGPS
logP	2.76	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	12.65	ChemAxon
pKa (Strongest Basic)	3.04	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	41.46 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	69.39 m³·mol⁻¹	ChemAxon
Polarizability	25.27 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	156.62	31661259
DarkChem	[M-H]-	151.565	31661259
DeepCCS	[M+H]+	153.388	30932474
DeepCCS	[M-H]-	151.03	30932474
DeepCCS	[M-2H]-	183.916	30932474
DeepCCS	[M+Na]+	159.481	30932474
AllCCS	[M+H]+	151.7	32859911
AllCCS	[M+H-H2O]+	147.9	32859911
AllCCS	[M+NH4]+	155.2	32859911
AllCCS	[M+Na]+	156.2	32859911
AllCCS	[M-H]-	155.0	32859911
AllCCS	[M+Na-2H]-	154.8	32859911
AllCCS	[M+HCOO]-	154.6	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	4.08 minutes	32390414
Predicted by Siyang on May 30, 2022	12.1834 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.19 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	28.6 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1812.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	347.2 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	119.8 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	205.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	111.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	429.7 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	692.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	102.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	951.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	357.5 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1317.2 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	306.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	395.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	444.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	180.3 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	95.3 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(S)-Spirobrassinin	CSC1=NCC2(S1)C(=O)NC1=C2C=CC=C1	3581.8	Standard polar	33892256
(S)-Spirobrassinin	CSC1=NCC2(S1)C(=O)NC1=C2C=CC=C1	2263.0	Standard non polar	33892256
(S)-Spirobrassinin	CSC1=NCC2(S1)C(=O)NC1=C2C=CC=C1	2453.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(S)-Spirobrassinin,1TMS,isomer #1	CSC1=NCC2(S1)C(=O)N([Si](C)(C)C)C1=CC=CC=C12	2306.8	Semi standard non polar	33892256
(S)-Spirobrassinin,1TMS,isomer #1	CSC1=NCC2(S1)C(=O)N([Si](C)(C)C)C1=CC=CC=C12	2125.3	Standard non polar	33892256
(S)-Spirobrassinin,1TBDMS,isomer #1	CSC1=NCC2(S1)C(=O)N([Si](C)(C)C(C)(C)C)C1=CC=CC=C12	2505.9	Semi standard non polar	33892256
(S)-Spirobrassinin,1TBDMS,isomer #1	CSC1=NCC2(S1)C(=O)N([Si](C)(C)C(C)(C)C)C1=CC=CC=C12	2398.3	Standard non polar	33892256

Spectra

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

FDB011345

KNApSAcK ID

Not Available

Chemspider ID

4930317

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6424827

PDB ID

Not Available

ChEBI ID

Not Available

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 (S)-Spirobrassinin (HMDB0035974)

MOL for HMDB0035974 ((S)-Spirobrassinin)

3D MOL for HMDB0035974 ((S)-Spirobrassinin)

3D SDF for HMDB0035974 ((S)-Spirobrassinin)

3D-SDF for HMDB0035974 ((S)-Spirobrassinin)

PDB for HMDB0035974 ((S)-Spirobrassinin)

3D PDB for HMDB0035974 ((S)-Spirobrassinin)

SMILES for HMDB0035974 ((S)-Spirobrassinin)

INCHI for HMDB0035974 ((S)-Spirobrassinin)

Structure for HMDB0035974 ((S)-Spirobrassinin)

3D Structure for HMDB0035974 ((S)-Spirobrassinin)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized