NP-MRD: Showing NP-Card for Cetoniacytone A (NP0004330)

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Record Information

Version

2.0

Created at

2020-12-09 01:49:28 UTC

Updated at

2021-07-15 16:48:53 UTC

NP-MRD ID

NP0004330

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cetoniacytone A

Provided By

NPAtlas

Description

Cetoniacytone A is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Cetoniacytone A is found in Actinomyces. Cetoniacytone A was first documented in 2002 (PMID: 12243453). Based on a literature review a small amount of articles have been published on cetoniacytone A (PMID: 19101977) (PMID: 17195255).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242118053D          

 26 27  0  0  0  0            999 V2000
    4.2236    1.1477   -0.2752 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8947    0.8787    0.3790 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6917    1.3557    1.5105 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9552    0.1113   -0.3081 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6656   -0.2436    0.1398 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1597    0.1081    1.2948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2187   -0.3702    1.5717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5152   -0.8019    2.6927 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1808   -0.2943    0.4459 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4025    0.5388    0.7581 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.1001    0.8971   -0.3798 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5427   -1.4983   -0.2224 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6144   -0.5645   -0.7740 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2042   -1.0912   -0.7312 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3412   -1.2300   -2.0045 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9798    1.1554    0.5176 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4646    0.2814   -0.9488 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2061    2.0789   -0.8664 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2644   -0.2344   -1.2735 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6808    0.7010    2.0253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1768    1.4264    1.3703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0794   -0.1159    1.3748 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3727    0.0489   -0.8358 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8920   -0.1310   -1.7565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1333   -2.1215   -0.2710 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9056   -2.0326   -2.0911 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  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
  7  9  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14  5  1  0  0  0  0
 13  9  1  0  0  0  0
  1 16  1  0  0  0  0
  1 17  1  0  0  0  0
  1 18  1  0  0  0  0
  4 19  1  0  0  0  0
  6 20  1  0  0  0  0
 10 21  1  0  0  0  0
 10 22  1  0  0  0  0
 11 23  1  0  0  0  0
 13 24  1  6  0  0  0
 14 25  1  1  0  0  0
 15 26  1  0  0  0  0
M  END


  Mrv1652306242118053D          

 26 27  0  0  0  0            999 V2000
    4.2236    1.1477   -0.2752 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8947    0.8787    0.3790 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6917    1.3557    1.5105 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9552    0.1113   -0.3081 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6656   -0.2436    0.1398 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1597    0.1081    1.2948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2187   -0.3702    1.5717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5152   -0.8019    2.6927 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1808   -0.2943    0.4459 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4025    0.5388    0.7581 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.1001    0.8971   -0.3798 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5427   -1.4983   -0.2224 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6144   -0.5645   -0.7740 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2042   -1.0912   -0.7312 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3412   -1.2300   -2.0045 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9798    1.1554    0.5176 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4646    0.2814   -0.9488 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2061    2.0789   -0.8664 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2644   -0.2344   -1.2735 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6808    0.7010    2.0253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1768    1.4264    1.3703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0794   -0.1159    1.3748 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3727    0.0489   -0.8358 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8920   -0.1310   -1.7565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1333   -2.1215   -0.2710 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9056   -2.0326   -2.0911 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  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
  7  9  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14  5  1  0  0  0  0
 13  9  1  0  0  0  0
  1 16  1  0  0  0  0
  1 17  1  0  0  0  0
  1 18  1  0  0  0  0
  4 19  1  0  0  0  0
  6 20  1  0  0  0  0
 10 21  1  0  0  0  0
 10 22  1  0  0  0  0
 11 23  1  0  0  0  0
 13 24  1  6  0  0  0
 14 25  1  1  0  0  0
 15 26  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0004330

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@@]12O[C@]1([H])[C@@]([H])(O[H])C(N([H])C(=O)C([H])([H])[H])=C([H])C2=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>
5

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
19.771326916899326

> <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]acetamide

> <ALOGPS_LOGP>
-0.80

> <JCHEM_LOGP>
-2.3205696356666663

> <ALOGPS_LOGS>
-0.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.789597494980569

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.973491843868768

> <JCHEM_PKA_STRONGEST_BASIC>
-3.188735094509015

> <JCHEM_POLAR_SURFACE_AREA>
99.16000000000001

> <JCHEM_REFRACTIVITY>
49.1424

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.82e+02 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]acetamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0       4.224   1.148  -0.275  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.895   0.879   0.379  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.692   1.356   1.510  0.00  0.00           O+0
HETATM    4  N   UNK     0       1.955   0.111  -0.308  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.666  -0.244   0.140  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.160   0.108   1.295  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.219  -0.370   1.572  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.515  -0.802   2.693  0.00  0.00           O+0
HETATM    9  C   UNK     0      -2.181  -0.294   0.446  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.402   0.539   0.758  0.00  0.00           C+0
HETATM   11  O   UNK     0      -4.100   0.897  -0.380  0.00  0.00           O+0
HETATM   12  O   UNK     0      -2.543  -1.498  -0.222  0.00  0.00           O+0
HETATM   13  C   UNK     0      -1.614  -0.565  -0.774  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.204  -1.091  -0.731  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.341  -1.230  -2.005  0.00  0.00           O+0
HETATM   16  H   UNK     0       4.980   1.155   0.518  0.00  0.00           H+0
HETATM   17  H   UNK     0       4.465   0.281  -0.949  0.00  0.00           H+0
HETATM   18  H   UNK     0       4.206   2.079  -0.866  0.00  0.00           H+0
HETATM   19  H   UNK     0       2.264  -0.234  -1.274  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.681   0.701   2.025  0.00  0.00           H+0
HETATM   21  H   UNK     0      -3.177   1.426   1.370  0.00  0.00           H+0
HETATM   22  H   UNK     0      -4.079  -0.116   1.375  0.00  0.00           H+0
HETATM   23  H   UNK     0      -4.373   0.049  -0.836  0.00  0.00           H+0
HETATM   24  H   UNK     0      -1.892  -0.131  -1.757  0.00  0.00           H+0
HETATM   25  H   UNK     0      -0.133  -2.122  -0.271  0.00  0.00           H+0
HETATM   26  H   UNK     0       0.906  -2.033  -2.091  0.00  0.00           H+0
CONECT    1    2   16   17   18                                             
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   19                                                  
CONECT    5    4    6   14                                                  
CONECT    6    5    7   20                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   12   13                                             
CONECT   10    9   11   21   22                                             
CONECT   11   10   23                                                       
CONECT   12    9   13                                                       
CONECT   13   12   14    9   24                                             
CONECT   14   13   15    5   25                                             
CONECT   15   14   26                                                       
CONECT   16    1                                                            
CONECT   17    1                                                            
CONECT   18    1                                                            
CONECT   19    4                                                            
CONECT   20    6                                                            
CONECT   21   10                                                            
CONECT   22   10                                                            
CONECT   23   11                                                            
CONECT   24   13                                                            
CONECT   25   14                                                            
CONECT   26   15                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   54    0
END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₉H₁₁NO₅

Average Mass

213.1890 Da

Monoisotopic Mass

213.06372 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

CC(=O)NC1=CC(=O)[C@]2(CO)O[C@@H]2[C@H]1O

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

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Actinomyces	NPAtlas	12243453

Species Where Detected

Species Name	Source	Reference
Actinomyces sp. (Strain Lu 9419)	KNApSAcK Database	22123792

Chemical Taxonomy

Classification

Not classified

Physical Properties

State

Not Available

Experimental 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

Predicted Properties

Property	Value	Source
logP	-0.8	ALOGPS
logP	-2.3	ChemAxon
logS	-0.07	ALOGPS
pKa (Strongest Acidic)	12.97	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	99.16 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	49.14 m³·mol⁻¹	ChemAxon
Polarizability	19.77 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

External Links

NPAtlas ID

NPA014963

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

Not Available

PDB ID

Not Available

ChEBI ID

84360

Good Scents ID

Not Available

References

General References

Schlorke O, Krastel P, Muller I, Uson I, Dettner K, Zeeck A: Structure and biosynthesis of cetoniacytone A, a cytotoxic aminocarba sugar produced by an endosymbiontic Actinomyces. J Antibiot (Tokyo). 2002 Jul;55(7):635-42. doi: 10.7164/antibiotics.55.635. [PubMed:12243453 ]
Wu X, Flatt PM, Xu H, Mahmud T: Biosynthetic gene cluster of cetoniacytone A, an unusual aminocyclitol from the endosymbiotic Bacterium Actinomyces sp. Lu 9419. Chembiochem. 2009 Jan 26;10(2):304-14. doi: 10.1002/cbic.200800527. [PubMed:19101977 ]
Wu X, Flatt PM, Schlorke O, Zeeck A, Dairi T, Mahmud T: A comparative analysis of the sugar phosphate cyclase superfamily involved in primary and secondary metabolism. Chembiochem. 2007 Jan 22;8(2):239-48. doi: 10.1002/cbic.200600446. [PubMed:17195255 ]

Showing NP-Card for Cetoniacytone A (NP0004330)

MOL for NP0004330 (Cetoniacytone A)

3D MOL for NP0004330 (Cetoniacytone A)

3D SDF for NP0004330 (Cetoniacytone A)

3D-SDF for NP0004330 (Cetoniacytone A)

PDB for NP0004330 (Cetoniacytone A)

3D PDB for NP0004330 (Cetoniacytone A)

SMILES for NP0004330 (Cetoniacytone A)

INCHI for NP0004330 (Cetoniacytone A)

Structure for NP0004330 (Cetoniacytone A)

3D Structure for NP0004330 (Cetoniacytone A)