MiMeDB: Showing metabocard for Deoxyakanthomycin (MMDBc0015454)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 06:17:00 UTC

Update Date

2025-10-07 16:06:25 UTC

Metabolite ID

MMDBc0015454

Metabolite Identification

Common Name

Deoxyakanthomycin

Description

Deoxyakanthomycin is a pyridone natural product belonging to the class of metabolites. This compound features an intricate structure characterized by a 7-membered carbocycle that contains five stereocenters, including one quaternary center, highlighting its stereochemical complexity (PMID:35297629 ). Recent research has demonstrated a computation-driven approach to its synthesis, utilizing a one-step process derived from a biosynthetic precursor. This innovative synthesis is based on computational analysis that predicted a σ-bridged cation mediated cyclization mechanism, which is crucial for the formation of deoxyakanthomycin (PMID:35297629 ). The ability to synthesize this compound efficiently not only underscores its significance in natural product chemistry but also opens avenues for further exploration of its biological activities and potential applications in drug development.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152108172D          

 24 25  0  0  1  0            999 V2000
   -2.9747    5.7155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3215    4.8971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7098    2.4925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6827    2.7288    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2779    2.1230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9923    2.5355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6942    5.1568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9225    4.3194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5100    5.0339    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0894    4.5957    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8327    3.3083    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4366    2.5355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1511    3.7730    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4366    3.3605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2779    3.7730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6211    3.5514    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9923    3.3605    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1511    2.1230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2779    4.5980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4369    3.4285    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3344    5.0030    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4256    4.1058    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4581    2.7701    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1202    2.9486    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
  9  1  1  6  0  0  0
  9  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  2  1  6  0  0  0
 10  7  1  0  0  0  0
 11  3  1  6  0  0  0
 12  5  1  0  0  0  0
 13 10  1  0  0  0  0
 13 11  1  0  0  0  0
 14 12  2  0  0  0  0
 13 14  1  1  0  0  0
 15 14  1  0  0  0  0
 16  4  1  6  0  0  0
 16  8  1  0  0  0  0
 16 11  1  0  0  0  0
 17  6  1  0  0  0  0
 17 15  2  0  0  0  0
 18 12  1  0  0  0  0
 19 15  1  0  0  0  0
 16 20  1  1  0  0  0
  9 21  1  1  0  0  0
 10 22  1  1  0  0  0
 11 23  1  1  0  0  0
 13 24  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0015454

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(C)C[C@]([H])(C)[C@@]([H])(C2=C(O)C=CN=C2O)[C@]([H])(C)[C@@](C)(O)C1

> <INCHI_IDENTIFIER>
InChI=1S/C16H25NO3/c1-9-7-10(2)13(11(3)16(4,20)8-9)14-12(18)5-6-17-15(14)19/h5-6,9-11,13,20H,7-8H2,1-4H3,(H2,17,18,19)/t9-,10+,11+,13-,16+/m1/s1

> <INCHI_KEY>
QLTWQIOYJXJUJH-WFEKMPBRSA-N

> <FORMULA>
C16H25NO3

> <MOLECULAR_WEIGHT>
279.38

> <EXACT_MASS>
279.183443669

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
45

> <JCHEM_AVERAGE_POLARIZABILITY>
30.83112177595256

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-[(1R,2S,3S,5R,7S)-3-hydroxy-2,3,5,7-tetramethylcycloheptyl]pyridine-2,4-diol

> <ALOGPS_LOGP>
2.80

> <JCHEM_LOGP>
3.1353273440000002

> <ALOGPS_LOGS>
-2.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.54674200495855

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.075669150056608

> <JCHEM_PKA_STRONGEST_BASIC>
1.6581558375789769

> <JCHEM_POLAR_SURFACE_AREA>
73.58000000000001

> <JCHEM_REFRACTIVITY>
78.8455

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.72e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(1R,2S,3S,5R,7S)-3-hydroxy-2,3,5,7-tetramethylcycloheptyl]pyridine-2,4-diol

> <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      -5.553  10.669   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.600   9.141   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.192   4.653   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.008   5.094   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.519   3.963   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.852   4.733   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.163   9.626   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.455   8.063   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.685   9.397   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.034   8.579   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.421   6.175   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.815   4.733   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.149   7.043   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.815   6.273   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.519   7.043   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.893   6.629   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       1.852   6.273   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0      -2.149   3.963   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.519   8.583   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -6.415   6.400   0.000  0.00  0.00           O+0
HETATM   21  H   UNK     0      -6.224   9.339   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0      -0.795   7.664   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0      -4.588   5.171   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0      -2.091   5.504   0.000  0.00  0.00           H+0
CONECT    1    9                                                            
CONECT    2   10                                                            
CONECT    3   11                                                            
CONECT    4   16                                                            
CONECT    5    6   12                                                       
CONECT    6    5   17                                                       
CONECT    7    9   10                                                       
CONECT    8    9   16                                                       
CONECT    9    1    7    8   21                                             
CONECT   10    2    7   13   22                                             
CONECT   11    3   13   16   23                                             
CONECT   12    5   14   18                                                  
CONECT   13   10   11   14   24                                             
CONECT   14   12   13   15                                                  
CONECT   15   14   17   19                                                  
CONECT   16    4    8   11   20                                             
CONECT   17    6   15                                                       
CONECT   18   12                                                            
CONECT   19   15                                                            
CONECT   20   16                                                            
CONECT   21    9                                                            
CONECT   22   10                                                            
CONECT   23   11                                                            
CONECT   24   13                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   50    0
END

Synonyms

Not Available

Molecular Formula

C₁₆H₂₅NO₃

Average Mass

279.38

Monoisotopic Mass

279.183443669

IUPAC Name

3-[(1R,2S,3S,5R,7S)-3-hydroxy-2,3,5,7-tetramethylcycloheptyl]pyridine-2,4-diol

Traditional Name

3-[(1R,2S,3S,5R,7S)-3-hydroxy-2,3,5,7-tetramethylcycloheptyl]pyridine-2,4-diol

CAS Registry Number

Not Available

SMILES

[H][C@@]1(C)C[C@]([H])(C)[C@@]([H])(C2=C(O)C=CN=C2O)[C@]([H])(C)[C@@](C)(O)C1

InChI Identifier

InChI=1S/C16H25NO3/c1-9-7-10(2)13(11(3)16(4,20)8-9)14-12(18)5-6-17-15(14)19/h5-6,9-11,13,20H,7-8H2,1-4H3,(H2,17,18,19)/t9-,10+,11+,13-,16+/m1/s1

InChI Key

QLTWQIOYJXJUJH-WFEKMPBRSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridinones. Pyridinones are compounds containing a pyridine ring, which bears a ketone.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Hydropyridines

Direct Parent

Pyridinones

Alternative Parents

Substituents

Dihydropyridine
Pyridinone
Hydroxypyridine
Cyclic alcohol
Tertiary alcohol
Vinylogous acid
Heteroaromatic compound
Lactam
Azacycle
Alcohol
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.67 g/L	ALOGPS
logP	2.8	ALOGPS
logP	3.14	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	7.08	ChemAxon
pKa (Strongest Basic)	1.66	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	73.58 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	78.85 m³·mol⁻¹	ChemAxon
Polarizability	30.83 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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
Eukaryota/Fungi	Ascomycota	1	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

24629760

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

45268808

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 Deoxyakanthomycin (MMDBc0015454)

MOL for #<Metabolite:0x00007f8d88cdecc8>

3D MOL for #<Metabolite:0x00007f8d88cdecc8>

3D SDF for #<Metabolite:0x00007f8d88cdecc8>

3D-SDF for #<Metabolite:0x00007f8d88cdecc8>

PDB for #<Metabolite:0x00007f8d88cdecc8>

3D PDB for #<Metabolite:0x00007f8d88cdecc8>

SMILES for #<Metabolite:0x00007f8d88cdecc8>

INCHI for #<Metabolite:0x00007f8d88cdecc8>

Structure for #<Metabolite:0x00007f8d88cdecc8>

3D Structure for #<Metabolite:0x00007f8d88cdecc8>