MiMeDB: Showing metabocard for Vibrindole A (MMDBc0015629)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 06:26:03 UTC

Update Date

2025-10-07 16:06:26 UTC

Metabolite ID

MMDBc0015629

Metabolite Identification

Common Name

Vibrindole A

Description

Vibrindole A is a bis(indolyl)methane derivative belonging to the class of indole alkaloids. This compound has garnered attention in the field of natural product chemistry due to its synthesis and potential biological activities. Various synthetic methodologies have been developed to access vibrindole A, including a protocol that highlights its utility in producing biologically active compounds alongside others like arundine and turbomycin B (PMID:38214898 ). The synthesis of vibrindole A has been achieved through innovative Friedel-Crafts reactions, utilizing halogen bond donors to facilitate the formation of bis(indolyl)methanes from indoles and aldehydes (PMID:31668078 ). Its structure has been confirmed through single crystal X-ray diffraction analysis (PMID:26120289 ). Additionally, vibrindole A has been implicated in exhibiting cytotoxic activity, indicating its potential as a lead compound in drug discovery (PMID:20431617 ). The exploration of vibrindole A and its derivatives continues to be an area of interest, particularly for their relevance in developing anti-inflammatory agents and other therapeutic applications (PMID:35060647 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004241518222D          

 20 23  0  0  0  0            999 V2000
    1.4358   -2.7631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -2.3215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2587   -3.0752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0792   -2.9890    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2508   -2.1820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9652   -1.7695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9652   -0.9445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2508   -0.5320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5363   -0.9445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5363   -1.7695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  3 11  1  0  0  0  0
  6 11  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 12 20  1  0  0  0  0
 15 20  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0015629

> <DATABASE_NAME>
MIME

> <SMILES>
CC(C1=CNC2=CC=CC=C12)C1=CNC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C18H16N2/c1-12(15-10-19-17-8-4-2-6-13(15)17)16-11-20-18-9-5-3-7-14(16)18/h2-12,19-20H,1H3

> <INCHI_KEY>
WOJBBIJJRKFKOJ-UHFFFAOYSA-N

> <FORMULA>
C18H16N2

> <MOLECULAR_WEIGHT>
260.34

> <EXACT_MASS>
260.131348523

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
29.75773775886976

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-[1-(1H-indol-3-yl)ethyl]-1H-indole

> <ALOGPS_LOGP>
4.93

> <JCHEM_LOGP>
4.549582925333333

> <ALOGPS_LOGS>
-5.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.06842577911525

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.40418258533343

> <JCHEM_POLAR_SURFACE_AREA>
31.58

> <JCHEM_REFRACTIVITY>
82.51680000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.90e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[1-(1H-indol-3-yl)ethyl]-1H-indole

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0       2.680  -5.158   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.143  -4.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.483  -5.740   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -2.015  -5.579   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -2.335  -4.073   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.668  -3.303   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.668  -1.763   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.335  -0.993   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.001  -1.763   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.001  -3.303   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    3    6                                                  
CONECT   12    2   13   20                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   12   15                                                  
MASTER        0    0    0    0    0    0    0    0   20    0   46    0
END

Synonyms

Value	Source
1,1-Di(3-indolyl)ethane	MeSH
Vibrindole a	MeSH
1,1-Bis(3'-indolyl)ethane	MeSH

Molecular Formula

C₁₈H₁₆N₂

Average Mass

260.34

Monoisotopic Mass

260.131348523

IUPAC Name

3-[1-(1H-indol-3-yl)ethyl]-1H-indole

Traditional Name

3-[1-(1H-indol-3-yl)ethyl]-1H-indole

CAS Registry Number

Not Available

SMILES

CC(C1=CNC2=CC=CC=C12)C1=CNC2=CC=CC=C12

InChI Identifier

InChI=1S/C18H16N2/c1-12(15-10-19-17-8-4-2-6-13(15)17)16-11-20-18-9-5-3-7-14(16)18/h2-12,19-20H,1H3

InChI Key

WOJBBIJJRKFKOJ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 3-alkylindoles. 3-Alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

3-alkylindoles

Alternative Parents

Substituents

3-alkylindole
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Azacycle
Organic nitrogen compound
Hydrocarbon derivative
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.00069 g/L	ALOGPS
logP	4.93	ALOGPS
logP	4.55	ChemAxon
logS	-5.6	ALOGPS
pKa (Strongest Acidic)	16.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	31.58 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	82.52 m³·mol⁻¹	ChemAxon
Polarizability	29.76 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

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
Bacteria/Eubacteria	Proteobacteria	1	Human	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6452189

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 Vibrindole A (MMDBc0015629)

MOL for #<Metabolite:0x00007f8dc531eb38>

3D MOL for #<Metabolite:0x00007f8dc531eb38>

3D SDF for #<Metabolite:0x00007f8dc531eb38>

3D-SDF for #<Metabolite:0x00007f8dc531eb38>

PDB for #<Metabolite:0x00007f8dc531eb38>

3D PDB for #<Metabolite:0x00007f8dc531eb38>

SMILES for #<Metabolite:0x00007f8dc531eb38>

INCHI for #<Metabolite:0x00007f8dc531eb38>

Structure for #<Metabolite:0x00007f8dc531eb38>

3D Structure for #<Metabolite:0x00007f8dc531eb38>