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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-23 06:36:51 UTC

Update Date

2021-09-23 06:36:51 UTC

HMDB ID

HMDB0302104

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Rapalexin A

Description

Rapalexin a is a member of the class of compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole. Rapalexin a is practically insoluble (in water) and a very weakly acidic compound (based on its pKa). Rapalexin a can be found in chinese cabbage, which makes rapalexin a a potential biomarker for the consumption of this food product.

Structure

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


  Mrv0541 02241212262D          

 14 15  0  0  0  0            999 V2000
   -1.7679    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4823    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4823   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7679   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0534   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0534    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2688    0.6675    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2688   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2161    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7679   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0534   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0138   -1.4520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8226   -1.4467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6476   -1.4511    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  2  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  7  6  1  0  0  0  0
  6  5  1  0  0  0  0
  5  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8  9  2  0  0  0  0
  4 10  1  0  0  0  0
 10 11  1  0  0  0  0
  8 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302104

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C2C(NC=C2N=C=S)=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C10H8N2OS/c1-13-9-4-2-3-7-10(9)8(5-11-7)12-6-14/h2-5,11H,1H3

> <INCHI_KEY>
DJDFPSQNQFBWJR-UHFFFAOYSA-N

> <FORMULA>
C10H8N2OS

> <MOLECULAR_WEIGHT>
204.248

> <EXACT_MASS>
204.035733578

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
20.97635410204564

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-isothiocyanato-4-methoxy-1H-indole

> <ALOGPS_LOGP>
3.13

> <JCHEM_LOGP>
2.936161770333333

> <ALOGPS_LOGS>
-3.71

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.319068107299135

> <JCHEM_PKA_STRONGEST_BASIC>
-0.5790813456142064

> <JCHEM_POLAR_SURFACE_AREA>
37.379999999999995

> <JCHEM_REFRACTIVITY>
60.6706

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.98e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-isothiocyanato-4-methoxy-1H-indole

> <JCHEM_VEBER_RULE>
1

$$$$

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  C   UNK     0      -3.300   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.634   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.634  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.300  -1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.966  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.966   0.770   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -0.502   1.246   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -0.502  -1.246   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.403   0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -3.300  -3.080   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -1.966  -3.850   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -0.026  -2.710   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       1.536  -2.701   0.000  0.00  0.00           C+0
HETATM   14  S   UNK     0       3.076  -2.709   0.000  0.00  0.00           S+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6    8                                                  
CONECT    6    1    7    5                                                  
CONECT    7    6    9                                                       
CONECT    8    5    9   12                                                  
CONECT    9    7    8                                                       
CONECT   10    4   11                                                       
CONECT   11   10                                                            
CONECT   12    8   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₀H₈N₂OS

Average Molecular Weight

204.248

Monoisotopic Molecular Weight

204.035733578

IUPAC Name

3-isothiocyanato-4-methoxy-1H-indole

Traditional Name

3-isothiocyanato-4-methoxy-1H-indole

CAS Registry Number

Not Available

SMILES

COC1=C2C(NC=C2N=C=S)=CC=C1

InChI Identifier

InChI=1S/C10H8N2OS/c1-13-9-4-2-3-7-10(9)8(5-11-7)12-6-14/h2-5,11H,1H3

InChI Key

DJDFPSQNQFBWJR-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
Anisole
Alkyl aryl ether
Substituted pyrrole
Benzenoid
Pyrrole
Heteroaromatic compound
Isothiocyanate
Propargyl-type 1,3-dipolar organic compound
Ether
Organic 1,3-dipolar compound
Azacycle
Organic oxygen compound
Hydrocarbon derivative
Organic nitrogen compound
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Chinese cabbage (FooDB: FOOD00035)

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
logP	3.13	ALOGPS
logP	2.94	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	14.32	ChemAxon
pKa (Strongest Basic)	-0.58	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	37.38 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	60.67 m³·mol⁻¹	ChemAxon
Polarizability	20.98 Å³	ChemAxon
Number of Rings	2	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
AllCCS	[M+H]+	142.338	32859911
AllCCS	[M+H-H2O]+	138.103	32859911
AllCCS	[M+Na]+	147.418	32859911
AllCCS	[M+NH4]+	146.282	32859911
AllCCS	[M-H]-	141.713	32859911
AllCCS	[M+Na-2H]-	141.936	32859911
AllCCS	[M+HCOO]-	142.267	32859911
DeepCCS	[M+H]+	140.453	30932474
DeepCCS	[M-H]-	138.057	30932474
DeepCCS	[M-2H]-	172.851	30932474
DeepCCS	[M+Na]+	147.371	30932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Rapalexin A,1TMS,isomer #1	COC1=CC=CC2=C1C(N=C=S)=CN2[Si](C)(C)C	2218.4	Semi standard non polar	33892256
Rapalexin A,1TMS,isomer #1	COC1=CC=CC2=C1C(N=C=S)=CN2[Si](C)(C)C	2207.7	Standard non polar	33892256
Rapalexin A,1TMS,isomer #1	COC1=CC=CC2=C1C(N=C=S)=CN2[Si](C)(C)C	3099.4	Standard polar	33892256
Rapalexin A,1TBDMS,isomer #1	COC1=CC=CC2=C1C(N=C=S)=CN2[Si](C)(C)C(C)(C)C	2408.8	Semi standard non polar	33892256
Rapalexin A,1TBDMS,isomer #1	COC1=CC=CC2=C1C(N=C=S)=CN2[Si](C)(C)C(C)(C)C	2409.4	Standard non polar	33892256
Rapalexin A,1TBDMS,isomer #1	COC1=CC=CC2=C1C(N=C=S)=CN2[Si](C)(C)C(C)(C)C	3142.1	Standard polar	33892256

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rapalexin A 10V, Positive-QTOF	splash10-0a4i-0190000000-17ebece94ceff500bd17	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rapalexin A 20V, Positive-QTOF	splash10-0a4i-0390000000-1a2e6be99fc407778167	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rapalexin A 40V, Positive-QTOF	splash10-00xs-2900000000-fafbc417a81c9f94e0cd	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rapalexin A 10V, Negative-QTOF	splash10-0udi-0090000000-16f53fce61bbf53ee25e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rapalexin A 20V, Negative-QTOF	splash10-0udi-0390000000-4887cc16fb02910f8af8	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rapalexin A 40V, Negative-QTOF	splash10-000i-2900000000-52923e9be5860b8af6e6	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rapalexin A 10V, Positive-QTOF	splash10-052b-0950000000-32192572c741792f860d	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rapalexin A 20V, Positive-QTOF	splash10-0a4j-0790000000-b8fc5de2f9596f8d7628	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rapalexin A 40V, Positive-QTOF	splash10-0bvi-6900000000-7556ca1472b258d62528	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rapalexin A 10V, Negative-QTOF	splash10-0udi-0090000000-f6d73d03e12d5fdebb7b	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rapalexin A 20V, Negative-QTOF	splash10-0pb9-7490000000-b37639baaac9349a6fb3	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Rapalexin A 40V, Negative-QTOF	splash10-0ab9-3900000000-b811bf14320514a3e82d	2021-10-21	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

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

FDB001862

KNApSAcK ID

C00034193

Chemspider ID

17260025

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

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

Not Available

Showing metabocard for Rapalexin A (HMDB0302104)

MOL for HMDB0302104 (Rapalexin A)

3D MOL for HMDB0302104 (Rapalexin A)

3D SDF for HMDB0302104 (Rapalexin A)

3D-SDF for HMDB0302104 (Rapalexin A)

PDB for HMDB0302104 (Rapalexin A)

3D PDB for HMDB0302104 (Rapalexin A)

SMILES for HMDB0302104 (Rapalexin A)

INCHI for HMDB0302104 (Rapalexin A)

Structure for HMDB0302104 (Rapalexin A)

3D Structure for HMDB0302104 (Rapalexin A)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

MS/MS Spectra