MiMeDB: Showing metabocard for Rimboxo (MMDBc0013877)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 05:04:36 UTC

Update Date

2025-10-07 16:06:12 UTC

Metabolite ID

MMDBc0013877

Metabolite Identification

Common Name

Rimboxo

Description

Rimboxo is a novel oxolane compound belonging to the class of metabolites. It was identified in a study involving the bacterium Enterobacter cloacae, which revealed Rimboxo as a unique chemical entity alongside three other known compounds (PMID:26252083 ). The presence of such metabolites in microbial systems highlights the intricate biochemical pathways and potential ecological roles they may play. While the primary focus of the research was on the chemical characterization of Rimboxo, its biological implications remain an area of interest, as metabolites often contribute to interactions within microbial communities and can have effects on host organisms. Further studies could elucidate the specific functions and mechanisms of action of Rimboxo, particularly in relation to its biosynthetic origins and potential applications in biotechnology or pharmacology. Understanding the chemistry of Rimboxo and its biological significance could provide insights into microbial metabolism and its contributions to environmental and health-related contexts.

Structure

MOL SDF PDB SMILES InChI

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       7.722   1.597   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.722   4.089   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.126   4.089   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       8.627   2.843   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.220   2.843   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.924   1.303   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       4.924   4.383   0.000  0.00  0.00           O+0
CONECT    1    5    9                                                       
CONECT    2    6    9                                                       
CONECT    3    7   10                                                       
CONECT    4    8   10                                                       
CONECT    5    1    6   11                                                  
CONECT    6    2    5   12                                                  
CONECT    7    3    8   11                                                  
CONECT    8    4    7   12                                                  
CONECT    9    1    2                                                       
CONECT   10    3    4                                                       
CONECT   11    5    7                                                       
CONECT   12    6    8                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   28    0
END

Synonyms

Not Available

Molecular Formula

C₈H₁₂O₄

Average Mass

172.18

Monoisotopic Mass

172.073558866

IUPAC Name

2,5,8,11-tetraoxatricyclo[7.3.0.0^{3,7}]dodecane

Traditional Name

2,5,8,11-tetraoxatricyclo[7.3.0.0^{3,7}]dodecane

CAS Registry Number

Not Available

SMILES

C1OCC2OC3COCC3OC12

InChI Identifier

InChI=1S/C8H12O4/c1-5-6(2-9-1)12-8-4-10-3-7(8)11-5/h5-8H,1-4H2

InChI Key

SSCNGZRUIGSXRM-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,4-dioxanes. These are organic compounds containing 1,4-dioxane, an aliphatic six-member ring with two oxygen atoms in ring positions 1 and 4.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Dioxanes

Sub Class

1,4-dioxanes

Direct Parent

1,4-dioxanes

Alternative Parents

Substituents

Para-dioxane
Tetrahydrofuran
Oxacycle
Ether
Dialkyl ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	250 g/L	ALOGPS
logP	-0.74	ALOGPS
logP	-0.29	ChemAxon
logS	0.16	ALOGPS
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	36.92 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	38.92 m³·mol⁻¹	ChemAxon
Polarizability	16.76 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View 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

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank	Species

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 ; Human feces	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

78444680

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139586854

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 Rimboxo (MMDBc0013877)

MOL for #<Metabolite:0x00007f2add60ab80>

3D MOL for #<Metabolite:0x00007f2add60ab80>

3D SDF for #<Metabolite:0x00007f2add60ab80>

3D-SDF for #<Metabolite:0x00007f2add60ab80>

PDB for #<Metabolite:0x00007f2add60ab80>

3D PDB for #<Metabolite:0x00007f2add60ab80>

SMILES for #<Metabolite:0x00007f2add60ab80>

INCHI for #<Metabolite:0x00007f2add60ab80>

Structure for #<Metabolite:0x00007f2add60ab80>

3D Structure for #<Metabolite:0x00007f2add60ab80>