MiMeDB: Showing metabocard for Debromomarinone (MMDBc0007311)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 00:32:35 UTC

Update Date

2025-10-07 16:05:18 UTC

Metabolite ID

MMDBc0007311

Metabolite Identification

Common Name

Debromomarinone

Description

Debromomarinone is a naphthoquinone-derived meroterpenoid, a chemical class that encompasses compounds combining both terpenoid and non-terpenoid structures. This metabolite has garnered attention in biomedical research due to its intriguing synthesis and biological implications. The total synthesis of debromomarinone was achieved through a series of pericyclic reactions, including an aromatic Claisen rearrangement and Diels-Alder reactions, highlighting its synthetic accessibility and structural complexity (PMID:31549845 ). In investigations of the strain CNQ-509, debromomarinone was isolated alongside novel naphterpin derivatives, further emphasizing its relevance in natural product chemistry (PMID:29534540 ). Additionally, the enzyme CnqP3, associated with the biosynthesis of tetrahydroxynaphthalene-derived natural products, has been implicated in the formation of debromomarinone, suggesting a biosynthetic pathway that contributes to its natural occurrence (PMID:26659564 ). The compound is also mentioned in the context of various other bioactive substances, indicating its potential significance in pharmacological research (PMID:7710421 ). Overall, debromomarinone represents a fascinating intersection of chemistry and biology, warranting further exploration of its properties and applications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152102322D          

 32 35  0  0  1  0            999 V2000
    1.2031    7.7462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9368    6.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1744    1.3284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4400    4.5772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5209    5.6728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5080    6.4977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0957    2.7316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1744    3.5111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2417    5.2715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2546    2.2639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2251    2.1079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3052    3.0434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2160    6.9213    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4444    2.1079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0352    2.2639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5246    3.0434    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6850    2.7316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9845    3.6671    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7651    3.6671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9550    3.5111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3347    3.1993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8748    2.5757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4149    4.1348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6048    3.9789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2546    4.4466    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.5753    1.6402    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0352    4.4466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6048    1.7961    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6850    4.9143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0647    4.6025    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7946    3.8230    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4444    4.2907    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  8  7  1  0  0  0  0
  9  5  1  0  0  0  0
 13  1  1  0  0  0  0
 13  2  1  0  0  0  0
 13  6  2  0  0  0  0
 14  3  1  0  0  0  0
 14  7  1  0  0  0  0
 14 10  2  0  0  0  0
 15 11  2  0  0  0  0
 15 12  1  0  0  0  0
 16 10  1  0  0  0  0
 17 11  1  0  0  0  0
 18  8  1  0  0  0  0
 18 16  1  0  0  0  0
 19 12  2  0  0  0  0
 20 17  2  0  0  0  0
 20 19  1  0  0  0  0
 21 16  1  0  0  0  0
 22 17  1  0  0  0  0
 22 21  1  0  0  0  0
 23 20  1  0  0  0  0
 24 21  2  0  0  0  0
 24 23  1  0  0  0  0
 25  4  1  1  0  0  0
 25  9  1  6  0  0  0
 25 18  1  0  0  0  0
 26 15  1  0  0  0  0
 27 19  1  0  0  0  0
 28 22  2  0  0  0  0
 29 23  2  0  0  0  0
 30 24  1  0  0  0  0
 30 25  1  0  0  0  0
 16 31  1  6  0  0  0
 18 32  1  6  0  0  0
M  END


  Mrv1652305152102322D          

 32 35  0  0  1  0            999 V2000
    1.2031    7.7462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9368    6.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1744    1.3284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4400    4.5772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5209    5.6728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5080    6.4977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0957    2.7316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1744    3.5111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2417    5.2715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2546    2.2639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2251    2.1079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3052    3.0434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2160    6.9213    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4444    2.1079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0352    2.2639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5246    3.0434    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6850    2.7316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9845    3.6671    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7651    3.6671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9550    3.5111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3347    3.1993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8748    2.5757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4149    4.1348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6048    3.9789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2546    4.4466    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.5753    1.6402    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0352    4.4466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6048    1.7961    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6850    4.9143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0647    4.6025    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7946    3.8230    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4444    4.2907    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  8  7  1  0  0  0  0
  9  5  1  0  0  0  0
 13  1  1  0  0  0  0
 13  2  1  0  0  0  0
 13  6  2  0  0  0  0
 14  3  1  0  0  0  0
 14  7  1  0  0  0  0
 14 10  2  0  0  0  0
 15 11  2  0  0  0  0
 15 12  1  0  0  0  0
 16 10  1  0  0  0  0
 17 11  1  0  0  0  0
 18  8  1  0  0  0  0
 18 16  1  0  0  0  0
 19 12  2  0  0  0  0
 20 17  2  0  0  0  0
 20 19  1  0  0  0  0
 21 16  1  0  0  0  0
 22 17  1  0  0  0  0
 22 21  1  0  0  0  0
 23 20  1  0  0  0  0
 24 21  2  0  0  0  0
 24 23  1  0  0  0  0
 25  4  1  1  0  0  0
 25  9  1  6  0  0  0
 25 18  1  0  0  0  0
 26 15  1  0  0  0  0
 27 19  1  0  0  0  0
 28 22  2  0  0  0  0
 29 23  2  0  0  0  0
 30 24  1  0  0  0  0
 30 25  1  0  0  0  0
 16 31  1  6  0  0  0
 18 32  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0007311

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]12CCC(C)=C[C@]1([H])C1=C(O[C@@]2(C)CCC=C(C)C)C(=O)C2=C(C=C(O)C=C2O)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H28O5/c1-13(2)6-5-9-25(4)18-8-7-14(3)10-16(18)21-22(28)17-11-15(26)12-19(27)20(17)23(29)24(21)30-25/h6,10-12,16,18,26-27H,5,7-9H2,1-4H3/t16-,18+,25-/m0/s1

> <INCHI_KEY>
DPALYVVGGATILJ-UVNWJPITSA-N

> <FORMULA>
C25H28O5

> <MOLECULAR_WEIGHT>
408.494

> <EXACT_MASS>
408.193674002

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
58

> <JCHEM_AVERAGE_POLARIZABILITY>
45.330546583877506

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4aR,5S,12bS)-8,10-dihydroxy-2,5-dimethyl-5-(4-methylpent-3-en-1-yl)-4,4a,5,7,12,12b-hexahydro-3H-6-oxatetraphene-7,12-dione

> <ALOGPS_LOGP>
4.30

> <JCHEM_LOGP>
4.891605949666666

> <ALOGPS_LOGS>
-4.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.814015183363324

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.216675086686458

> <JCHEM_PKA_STRONGEST_BASIC>
-5.00418209573455

> <JCHEM_POLAR_SURFACE_AREA>
83.83

> <JCHEM_REFRACTIVITY>
118.69129999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.05e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4aR,5S,12bS)-8,10-dihydroxy-2,5-dimethyl-5-(4-methylpent-3-en-1-yl)-3,4,4a,12b-tetrahydro-6-oxatetraphene-7,12-dione

> <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       2.246  14.460   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.615  12.171   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.326   2.480   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.821   8.544   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.972  10.589   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.948  12.129   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.179   5.099   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.326   6.554   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.318   9.840   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.342   4.226   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.887   3.935   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.903   5.681   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.270  12.920   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.830   3.935   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.399   4.226   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.846   5.681   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.879   5.099   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.838   6.845   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.895   6.845   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.383   6.554   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.358   5.972   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.366   4.808   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.375   7.718   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.862   7.427   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.342   8.300   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      10.407   3.062   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       9.399   8.300   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       4.862   3.353   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       6.879   9.173   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       3.854   8.591   0.000  0.00  0.00           O+0
HETATM   31  H   UNK     0       3.350   7.136   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0       0.830   8.009   0.000  0.00  0.00           H+0
CONECT    1   13                                                            
CONECT    2   13                                                            
CONECT    3   14                                                            
CONECT    4   25                                                            
CONECT    5    6    9                                                       
CONECT    6    5   13                                                       
CONECT    7    8   14                                                       
CONECT    8    7   18                                                       
CONECT    9    5   25                                                       
CONECT   10   14   16                                                       
CONECT   11   15   17                                                       
CONECT   12   15   19                                                       
CONECT   13    1    2    6                                                  
CONECT   14    3    7   10                                                  
CONECT   15   11   12   26                                                  
CONECT   16   10   18   21   31                                             
CONECT   17   11   20   22                                                  
CONECT   18    8   16   25   32                                             
CONECT   19   12   20   27                                                  
CONECT   20   17   19   23                                                  
CONECT   21   16   22   24                                                  
CONECT   22   17   21   28                                                  
CONECT   23   20   24   29                                                  
CONECT   24   21   23   30                                                  
CONECT   25    4    9   18   30                                             
CONECT   26   15                                                            
CONECT   27   19                                                            
CONECT   28   22                                                            
CONECT   29   23                                                            
CONECT   30   24   25                                                       
CONECT   31   16                                                            
CONECT   32   18                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   70    0
END

Synonyms

Not Available

Molecular Formula

C₂₅H₂₈O₅

Average Mass

408.494

Monoisotopic Mass

408.193674002

IUPAC Name

(4aR,5S,12bS)-8,10-dihydroxy-2,5-dimethyl-5-(4-methylpent-3-en-1-yl)-4,4a,5,7,12,12b-hexahydro-3H-6-oxatetraphene-7,12-dione

Traditional Name

(4aR,5S,12bS)-8,10-dihydroxy-2,5-dimethyl-5-(4-methylpent-3-en-1-yl)-3,4,4a,12b-tetrahydro-6-oxatetraphene-7,12-dione

CAS Registry Number

Not Available

SMILES

[H][C@@]12CCC(C)=C[C@]1([H])C1=C(O[C@@]2(C)CCC=C(C)C)C(=O)C2=C(C=C(O)C=C2O)C1=O

InChI Identifier

InChI=1S/C25H28O5/c1-13(2)6-5-9-25(4)18-8-7-14(3)10-16(18)21-22(28)17-11-15(26)12-19(27)20(17)23(29)24(21)30-25/h6,10-12,16,18,26-27H,5,7-9H2,1-4H3/t16-,18+,25-/m0/s1

InChI Key

DPALYVVGGATILJ-UVNWJPITSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as naphthopyranones. Naphthopyranones are compounds containing a naphthopyran skeleton where a ring carbon bears a carboxylic acid group. Naphthtopyran is made up of the pyran ring fused to a naphthalene ring system.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Naphthopyrans

Sub Class

Naphthopyranones

Direct Parent

Naphthopyranones

Alternative Parents

Substituents

Naphthopyranone
Naphthoquinone
Naphthalene
Aryl ketone
Quinone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Phenol
Benzenoid
Pyran
Vinylogous ester
Vinylogous acid
Ketone
Oxacycle
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
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	0.007 g/L	ALOGPS
logP	4.3	ALOGPS
logP	4.89	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	7.22	ChemAxon
pKa (Strongest Basic)	-5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	83.83 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	118.69 m³·mol⁻¹	ChemAxon
Polarizability	45.33 Å³	ChemAxon
Number of Rings	4	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

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	Actinobacteria	1	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

Not Available

Chemspider ID

8584615

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Debromomarinone

METLIN ID

Not Available

PubChem Compound

10409178

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 Debromomarinone (MMDBc0007311)

MOL for #<Metabolite:0x00007f2ac0c5f610>

3D MOL for #<Metabolite:0x00007f2ac0c5f610>

3D SDF for #<Metabolite:0x00007f2ac0c5f610>

3D-SDF for #<Metabolite:0x00007f2ac0c5f610>

PDB for #<Metabolite:0x00007f2ac0c5f610>

3D PDB for #<Metabolite:0x00007f2ac0c5f610>

SMILES for #<Metabolite:0x00007f2ac0c5f610>

INCHI for #<Metabolite:0x00007f2ac0c5f610>

Structure for #<Metabolite:0x00007f2ac0c5f610>

3D Structure for #<Metabolite:0x00007f2ac0c5f610>