MiMeDB: Showing metabocard for Cetoniacytone A (MMDBc0015204)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 06:05:26 UTC

Update Date

2025-10-07 16:06:22 UTC

Metabolite ID

MMDBc0015204

Metabolite Identification

Common Name

Cetoniacytone A

Description

Cetoniacytone A is a unique aminocyclitol antibiotic belonging to the chemical class of C(7)N-aminocyclitols. This metabolite has garnered attention due to its cytotoxic properties and its production by the endosymbiotic bacterium Actinomyces sp. The biosynthetic gene cluster responsible for cetoniacytone A was identified, highlighting its potential as an antitumor agent (PMID:19101977 ). Feeding experiments utilizing isotopically labeled cyclitols indicated that cetoniacytone A is derived from 2-epi-5-epi-valiolone, a product of the shikimic acid pathway (SPC) (PMID:17195255 ). The structure and biosynthesis of cetoniacytone A have been characterized, revealing its role as a cytotoxic aminocarba sugar produced by Actinomyces sp. (PMID:12243453 ). Furthermore, cetoniacytone A and several related minor components were successfully produced by this bacterial strain, underscoring its significance in the realm of natural product chemistry and potential therapeutic applications (PMID:12243453 ). The exploration of cetoniacytone A not only enhances our understanding of aminocyclitol antibiotics but also opens avenues for further research into its biological activities and mechanisms of action.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152108052D          

 17 18  0  0  1  0            999 V2000
    4.2868    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164    0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164    2.3645    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  2  2  0  0  0  0
  6  2  1  0  0  0  0
  7  5  1  0  0  0  0
  8  7  1  0  0  0  0
  9  3  1  1  0  0  0
  9  6  1  0  0  0  0
  9  8  1  0  0  0  0
 10  4  2  0  0  0  0
 10  5  1  4  0  0  0
 11  3  1  0  0  0  0
 12  4  1  0  0  0  0
 13  6  2  0  0  0  0
  7 14  1  1  0  0  0
 15  8  1  0  0  0  0
 15  9  1  0  0  0  0
  7 16  1  6  0  0  0
  8 17  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0015204

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]12O[C@@]1(CO)C(=O)C=C(N=C(C)O)[C@]2([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C9H11NO5/c1-4(12)10-5-2-6(13)9(3-11)8(15-9)7(5)14/h2,7-8,11,14H,3H2,1H3,(H,10,12)/t7-,8+,9-/m0/s1

> <INCHI_KEY>
JYYJQJKNUQRQSW-YIZRAAEISA-N

> <FORMULA>
C9H11NO5

> <MOLECULAR_WEIGHT>
213.189

> <EXACT_MASS>
213.063722458

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
19.83134640387008

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(1R,2S,6R)-2-hydroxy-6-(hydroxymethyl)-5-oxo-7-oxabicyclo[4.1.0]hept-3-en-3-yl]ethanimidic acid

> <ALOGPS_LOGP>
-1.02

> <JCHEM_LOGP>
-1.5009655086666664

> <ALOGPS_LOGS>
-1.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.280639284181515

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.491210673936604

> <JCHEM_PKA_STRONGEST_BASIC>
2.4789206718347363

> <JCHEM_POLAR_SURFACE_AREA>
102.65000000000002

> <JCHEM_REFRACTIVITY>
49.6641

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.96e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(1R,2S,6R)-2-hydroxy-6-(hydroxymethyl)-5-oxo-7-oxabicyclo[4.1.0]hept-3-en-3-yl]ethanimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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       8.002   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.897   0.206   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.668   5.390   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335   3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       6.668   3.850   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       2.667  -1.127   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       5.335   6.160   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       4.001   5.390   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM   16  H   UNK     0       5.335   4.620   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0       1.897   4.414   0.000  0.00  0.00           H+0
CONECT    1    4                                                            
CONECT    2    5    6                                                       
CONECT    3    9   11                                                       
CONECT    4    1   10   12                                                  
CONECT    5    2    7   10                                                  
CONECT    6    2    9   13                                                  
CONECT    7    5    8   14   16                                             
CONECT    8    7    9   15   17                                             
CONECT    9    3    6    8   15                                             
CONECT   10    4    5                                                       
CONECT   11    3                                                            
CONECT   12    4                                                            
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15    8    9                                                       
CONECT   16    7                                                            
CONECT   17    8                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

Synonyms

Not Available

Molecular Formula

C₉H₁₁NO₅

Average Mass

213.189

Monoisotopic Mass

213.063722458

IUPAC Name

N-[(1R,2S,6R)-2-hydroxy-6-(hydroxymethyl)-5-oxo-7-oxabicyclo[4.1.0]hept-3-en-3-yl]ethanimidic acid

Traditional Name

N-[(1R,2S,6R)-2-hydroxy-6-(hydroxymethyl)-5-oxo-7-oxabicyclo[4.1.0]hept-3-en-3-yl]ethanimidic acid

CAS Registry Number

Not Available

SMILES

[H][C@]12O[C@@]1(CO)C(=O)C=C(N=C(C)O)[C@]2([H])O

InChI Identifier

InChI=1S/C9H11NO5/c1-4(12)10-5-2-6(13)9(3-11)8(15-9)7(5)14/h2,7-8,11,14H,3H2,1H3,(H,10,12)/t7-,8+,9-/m0/s1

InChI Key

JYYJQJKNUQRQSW-YIZRAAEISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclohexenones. Cyclohexenones are compounds containing a cylohexenone moiety, which is a six-membered aliphatic ring that carries a ketone and has one endocyclic double bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Cyclohexenones

Alternative Parents

Substituents

Cyclohexenone
Vinylogous amide
Acetamide
Carboxamide group
Secondary alcohol
Secondary carboxylic acid amide
Carboxylic acid derivative
Dialkyl ether
Oxirane
Ether
Organoheterocyclic compound
Oxacycle
Organonitrogen compound
Alcohol
Primary alcohol
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic nitrogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

tertiary alcohol (CHEBI:84360 )
epoxide (CHEBI:84360 )
enone (CHEBI:84360 )
primary alcohol (CHEBI:84360 )
oxabicycloalkane (CHEBI:84360 )
acetamide (CHEBI:84360 )
cyclohexenones (CHEBI:84360 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	8.96 g/L	ALOGPS
logP	-1	ALOGPS
logP	-1.5	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	5.49	ChemAxon
pKa (Strongest Basic)	2.48	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	102.65 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	49.66 m³·mol⁻¹	ChemAxon
Polarizability	19.83 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	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	Actinobacteria	2	Human ; Human feces; Human saliva; Human urine; Human supragingival plaque; Human sputum; Human subgingival plaque	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

C00015074

Chemspider ID

8641204

KEGG Compound ID

Not Available

BioCyc ID

CPD-17535

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10465793

PDB ID

Not Available

ChEBI ID

84360

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 Cetoniacytone A (MMDBc0015204)

MOL for #<Metabolite:0x00007f8dc1069838>

3D MOL for #<Metabolite:0x00007f8dc1069838>

3D SDF for #<Metabolite:0x00007f8dc1069838>

3D-SDF for #<Metabolite:0x00007f8dc1069838>

PDB for #<Metabolite:0x00007f8dc1069838>

3D PDB for #<Metabolite:0x00007f8dc1069838>

SMILES for #<Metabolite:0x00007f8dc1069838>

INCHI for #<Metabolite:0x00007f8dc1069838>

Structure for #<Metabolite:0x00007f8dc1069838>

3D Structure for #<Metabolite:0x00007f8dc1069838>