MiMeDB: Showing metabocard for Hydroxydebromomarinone (MMDBc0012746)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 04:12:06 UTC

Update Date

2022-08-31 06:34:56 UTC

Metabolite ID

MMDBc0012746

Metabolite Identification

Common Name

Hydroxydebromomarinone

Description

Hydroxydebromomarinone 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. Hydroxydebromomarinone is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152106122D          

 32 35  0  0  1  0            999 V2000
    4.0063    7.7239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7014    6.4754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0420    1.3372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3407    4.5772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2597    5.6728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2726    6.4977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6062    3.5111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5389    5.2715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8763    2.7316    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
   -1.5246    3.0434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5261    2.2639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    6.8990    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
    0.0957    2.7316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2560    3.0434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7961    3.6671    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9845    3.6671    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
    1.4459    3.1993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9058    2.5757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3657    4.1348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1758    3.9789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3362    2.1079    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5261    4.4466    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7946    1.6402    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2546    4.4466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1758    1.7961    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0957    4.9143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0442    1.6844    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7159    4.6025    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9860    3.8230    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  8  5  1  0  0  0  0
  9  7  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 10  2  0  0  0  0
 14 11  1  0  0  0  0
 15 10  1  0  0  0  0
 16 12  2  0  0  0  0
 17  7  1  0  0  0  0
 17 16  1  0  0  0  0
 18 11  2  0  0  0  0
 19 15  2  0  0  0  0
 19 18  1  0  0  0  0
 20 16  1  0  0  0  0
 21 15  1  0  0  0  0
 21 20  1  0  0  0  0
 22 19  1  0  0  0  0
 23 20  2  0  0  0  0
 23 22  1  0  0  0  0
 24  3  1  1  0  0  0
 24  9  1  0  0  0  0
 24 12  1  0  0  0  0
 25  4  1  6  0  0  0
 25  8  1  1  0  0  0
 25 17  1  0  0  0  0
 26 14  1  0  0  0  0
 27 18  1  0  0  0  0
 28 21  2  0  0  0  0
 29 22  2  0  0  0  0
 24 30  1  6  0  0  0
 31 23  1  0  0  0  0
 31 25  1  0  0  0  0
 17 32  1  1  0  0  0
M  END


  Mrv1652305152106122D          

 32 35  0  0  1  0            999 V2000
    4.0063    7.7239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7014    6.4754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0420    1.3372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3407    4.5772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2597    5.6728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2726    6.4977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6062    3.5111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5389    5.2715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8763    2.7316    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
   -1.5246    3.0434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5261    2.2639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    6.8990    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
    0.0957    2.7316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2560    3.0434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7961    3.6671    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9845    3.6671    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
    1.4459    3.1993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9058    2.5757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3657    4.1348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1758    3.9789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3362    2.1079    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5261    4.4466    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7946    1.6402    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2546    4.4466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1758    1.7961    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0957    4.9143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0442    1.6844    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7159    4.6025    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9860    3.8230    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  8  5  1  0  0  0  0
  9  7  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 10  2  0  0  0  0
 14 11  1  0  0  0  0
 15 10  1  0  0  0  0
 16 12  2  0  0  0  0
 17  7  1  0  0  0  0
 17 16  1  0  0  0  0
 18 11  2  0  0  0  0
 19 15  2  0  0  0  0
 19 18  1  0  0  0  0
 20 16  1  0  0  0  0
 21 15  1  0  0  0  0
 21 20  1  0  0  0  0
 22 19  1  0  0  0  0
 23 20  2  0  0  0  0
 23 22  1  0  0  0  0
 24  3  1  1  0  0  0
 24  9  1  0  0  0  0
 24 12  1  0  0  0  0
 25  4  1  6  0  0  0
 25  8  1  1  0  0  0
 25 17  1  0  0  0  0
 26 14  1  0  0  0  0
 27 18  1  0  0  0  0
 28 21  2  0  0  0  0
 29 22  2  0  0  0  0
 24 30  1  6  0  0  0
 31 23  1  0  0  0  0
 31 25  1  0  0  0  0
 17 32  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0012746

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]12CC[C@](C)(O)C=C1C1=C(O[C@@]2(C)CCC=C(C)C)C(=O)C2=C(C=C(O)C=C2O)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H28O6/c1-13(2)6-5-8-25(4)17-7-9-24(3,30)12-16(17)20-21(28)15-10-14(26)11-18(27)19(15)22(29)23(20)31-25/h6,10-12,17,26-27,30H,5,7-9H2,1-4H3/t17-,24+,25+/m1/s1

> <INCHI_KEY>
MUPLWVKSOMVFQB-XATISFHKSA-N

> <FORMULA>
C25H28O6

> <MOLECULAR_WEIGHT>
424.493

> <EXACT_MASS>
424.188588622

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
45.643269282052394

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
3.91

> <JCHEM_LOGP>
3.6543524546666664

> <ALOGPS_LOGS>
-4.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.800583574865305

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.202657868719553

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2761264971774624

> <JCHEM_POLAR_SURFACE_AREA>
104.06

> <JCHEM_REFRACTIVITY>
120.29639999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.17e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4aR,5S)-2,8,10-trihydroxy-2,5-dimethyl-5-(4-methylpent-3-en-1-yl)-4,4a-dihydro-3H-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       7.478  14.418   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.776  12.087   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.678   2.496   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.236   8.544   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.085  10.589   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.109  12.129   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.732   6.554   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.739   9.840   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.236   5.099   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.830   3.935   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.846   5.681   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.715   4.226   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.454  12.878   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.342   4.226   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.179   5.099   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.211   5.681   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.219   6.845   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      -0.326   6.554   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.699   5.972   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.691   4.808   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.683   7.718   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.195   7.427   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.228   3.935   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.715   8.300   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -3.350   3.062   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -2.342   8.300   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       2.195   3.353   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.179   9.173   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       7.549   3.144   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       3.203   8.591   0.000  0.00  0.00           O+0
HETATM   32  H   UNK     0       3.707   7.136   0.000  0.00  0.00           H+0
CONECT    1   13                                                            
CONECT    2   13                                                            
CONECT    3   24                                                            
CONECT    4   25                                                            
CONECT    5    6    8                                                       
CONECT    6    5   13                                                       
CONECT    7    9   17                                                       
CONECT    8    5   25                                                       
CONECT    9    7   24                                                       
CONECT   10   14   15                                                       
CONECT   11   14   18                                                       
CONECT   12   16   24                                                       
CONECT   13    1    2    6                                                  
CONECT   14   10   11   26                                                  
CONECT   15   10   19   21                                                  
CONECT   16   12   17   20                                                  
CONECT   17    7   16   25   32                                             
CONECT   18   11   19   27                                                  
CONECT   19   15   18   22                                                  
CONECT   20   16   21   23                                                  
CONECT   21   15   20   28                                                  
CONECT   22   19   23   29                                                  
CONECT   23   20   22   31                                                  
CONECT   24    3    9   12   30                                             
CONECT   25    4    8   17   31                                             
CONECT   26   14                                                            
CONECT   27   18                                                            
CONECT   28   21                                                            
CONECT   29   22                                                            
CONECT   30   24                                                            
CONECT   31   23   25                                                       
CONECT   32   17                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   70    0
END

Synonyms

Not Available

Molecular Formula

C₂₅H₂₈O₆

Average Mass

424.493

Monoisotopic Mass

424.188588622

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

[H][C@@]12CC[C@](C)(O)C=C1C1=C(O[C@@]2(C)CCC=C(C)C)C(=O)C2=C(C=C(O)C=C2O)C1=O

InChI Identifier

InChI=1S/C25H28O6/c1-13(2)6-5-8-25(4)17-7-9-24(3,30)12-16(17)20-21(28)15-10-14(26)11-18(27)19(15)22(29)23(20)31-25/h6,10-12,17,26-27,30H,5,7-9H2,1-4H3/t17-,24+,25+/m1/s1

InChI Key

MUPLWVKSOMVFQB-XATISFHKSA-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
Quinone
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Pyranone
Benzenoid
Pyran
Tertiary alcohol
Vinylogous acid
Vinylogous ester
Ketone
Polyol
Oxacycle
Alcohol
Organic oxide
Organooxygen compound
Organic oxygen compound
Hydrocarbon derivative
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	0.012 g/L	ALOGPS
logP	3.91	ALOGPS
logP	3.65	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	7.2	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	104.06 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	120.3 m³·mol⁻¹	ChemAxon
Polarizability	45.64 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

Metabolic Reactions

Not Available

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	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	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

8223546

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10047983

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

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 Hydroxydebromomarinone (MMDBc0012746)

MOL for #<Metabolite:0x00007fed153b01c8>

3D MOL for #<Metabolite:0x00007fed153b01c8>

3D SDF for #<Metabolite:0x00007fed153b01c8>

3D-SDF for #<Metabolite:0x00007fed153b01c8>

PDB for #<Metabolite:0x00007fed153b01c8>

3D PDB for #<Metabolite:0x00007fed153b01c8>

SMILES for #<Metabolite:0x00007fed153b01c8>

INCHI for #<Metabolite:0x00007fed153b01c8>

Structure for #<Metabolite:0x00007fed153b01c8>

3D Structure for #<Metabolite:0x00007fed153b01c8>