MiMeDB: Showing metabocard for Hatomarubigin F (MMDBc0017430)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 07:48:58 UTC

Update Date

2025-10-07 16:06:41 UTC

Metabolite ID

MMDBc0017430

Metabolite Identification

Common Name

Hatomarubigin F

Description

Hatomarubigin F is a secondary metabolite classified within the polyketide chemical class. Its chemical structure features a complex arrangement of carbon chains and functional groups characteristic of polyketides, which are synthesized through the action of polyketide synthases. Hatomarubigin F is produced by the actinobacterium Streptomyces lividans, specifically in a genetic context where the hrb genes are expressed, although the hrbF gene is absent (PMID:24129687 ). This compound is involved in various biosynthetic pathways, contributing to the organism's metabolic diversity. Polyketides like hatomarubigin F often play roles in ecological interactions, such as antimicrobial activity, though the precise biological pathways in which hatomarubigin F participates remain to be fully elucidated. The study of such metabolites can provide insights into the genetic and enzymatic mechanisms underlying their biosynthesis, as well as their potential applications in biotechnology and medicine.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152109482D          

 25 28  0  0  0  0            999 V2000
    6.8298    1.9618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188    1.4941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8889    2.2736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7497    1.0264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4796    2.4296    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8593   -0.0650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0197    1.8059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9395    0.8704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3193    0.5586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589    0.8704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990    2.4296    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6695    0.0909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6695    2.2736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3994    1.4941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5893    1.3382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9690    1.0264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2391    1.8059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5091    0.4027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0492    1.9618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8889    0.0909    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9690    3.2091    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2096   -0.5327    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1294    2.8973    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2391   -0.3768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3193    2.7414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  7  1  1  0  0  0  0
  7  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  4  1  0  0  0  0
  9  6  2  0  0  0  0
 10  2  1  0  0  0  0
 11  3  1  0  0  0  0
 12  6  1  0  0  0  0
 12  8  2  0  0  0  0
 13  5  1  0  0  0  0
 14  8  1  0  0  0  0
 14 13  1  0  0  0  0
 15  9  1  0  0  0  0
 15 14  2  0  0  0  0
 16 10  2  0  0  0  0
 17 11  2  0  0  0  0
 17 16  1  0  0  0  0
 18  9  1  0  0  0  0
 18 16  1  0  0  0  0
 19 15  1  0  0  0  0
 19 17  1  0  0  0  0
 20 10  1  0  0  0  0
 21 11  1  0  0  0  0
 22 12  1  0  0  0  0
 23 13  1  0  0  0  0
 24 18  2  0  0  0  0
 25 19  2  0  0  0  0
M  END


  Mrv1652305152109482D          

 25 28  0  0  0  0            999 V2000
    6.8298    1.9618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188    1.4941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8889    2.2736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7497    1.0264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4796    2.4296    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8593   -0.0650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0197    1.8059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9395    0.8704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3193    0.5586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589    0.8704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990    2.4296    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6695    0.0909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6695    2.2736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3994    1.4941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5893    1.3382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9690    1.0264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2391    1.8059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5091    0.4027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0492    1.9618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8889    0.0909    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9690    3.2091    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2096   -0.5327    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1294    2.8973    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2391   -0.3768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3193    2.7414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  7  1  1  0  0  0  0
  7  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  4  1  0  0  0  0
  9  6  2  0  0  0  0
 10  2  1  0  0  0  0
 11  3  1  0  0  0  0
 12  6  1  0  0  0  0
 12  8  2  0  0  0  0
 13  5  1  0  0  0  0
 14  8  1  0  0  0  0
 14 13  1  0  0  0  0
 15  9  1  0  0  0  0
 15 14  2  0  0  0  0
 16 10  2  0  0  0  0
 17 11  2  0  0  0  0
 17 16  1  0  0  0  0
 18  9  1  0  0  0  0
 18 16  1  0  0  0  0
 19 15  1  0  0  0  0
 19 17  1  0  0  0  0
 20 10  1  0  0  0  0
 21 11  1  0  0  0  0
 22 12  1  0  0  0  0
 23 13  1  0  0  0  0
 24 18  2  0  0  0  0
 25 19  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0017430

> <DATABASE_NAME>
MIME

> <SMILES>
CC1CC(O)C2=C3C(=O)C4=C(O)C=CC(O)=C4C(=O)C3=CC(O)=C2C1

> <INCHI_IDENTIFIER>
InChI=1S/C19H16O6/c1-7-4-8-12(22)6-9-15(14(8)13(23)5-7)19(25)17-11(21)3-2-10(20)16(17)18(9)24/h2-3,6-7,13,20-23H,4-5H2,1H3

> <INCHI_KEY>
NXMMIDHKNNDZHM-UHFFFAOYSA-N

> <FORMULA>
C19H16O6

> <MOLECULAR_WEIGHT>
340.331

> <EXACT_MASS>
340.094688235

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
34.54781859488699

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1,5,8,11-tetrahydroxy-3-methyl-1,2,3,4,7,12-hexahydrotetraphene-7,12-dione

> <ALOGPS_LOGP>
2.36

> <JCHEM_LOGP>
3.8164723449999993

> <ALOGPS_LOGS>
-3.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.539901299612145

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.39941047026453

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2028562264354896

> <JCHEM_POLAR_SURFACE_AREA>
115.06

> <JCHEM_REFRACTIVITY>
90.63999999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.48e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,5,8,11-tetrahydroxy-3-methyl-1,2,3,4-tetrahydrotetraphene-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      12.749   3.662   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.155   2.789   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.659   4.244   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.733   1.916   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.229   4.535   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.204  -0.121   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      11.237   3.371   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.220   1.625   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.196   1.043   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.163   1.625   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.171   4.535   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.716   0.170   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.716   4.244   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.212   2.789   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.700   2.498   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.676   1.916   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.180   3.371   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.684   0.752   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.692   3.662   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.659   0.170   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       3.676   5.990   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       9.725  -0.994   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       7.708   5.408   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.180  -0.703   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       6.196   5.117   0.000  0.00  0.00           O+0
CONECT    1    7                                                            
CONECT    2    3   10                                                       
CONECT    3    2   11                                                       
CONECT    4    7    8                                                       
CONECT    5    7   13                                                       
CONECT    6    9   12                                                       
CONECT    7    1    4    5                                                  
CONECT    8    4   12   14                                                  
CONECT    9    6   15   18                                                  
CONECT   10    2   16   20                                                  
CONECT   11    3   17   21                                                  
CONECT   12    6    8   22                                                  
CONECT   13    5   14   23                                                  
CONECT   14    8   13   15                                                  
CONECT   15    9   14   19                                                  
CONECT   16   10   17   18                                                  
CONECT   17   11   16   19                                                  
CONECT   18    9   16   24                                                  
CONECT   19   15   17   25                                                  
CONECT   20   10                                                            
CONECT   21   11                                                            
CONECT   22   12                                                            
CONECT   23   13                                                            
CONECT   24   18                                                            
CONECT   25   19                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   56    0
END

Synonyms

Not Available

Molecular Formula

C₁₉H₁₆O₆

Average Mass

340.331

Monoisotopic Mass

340.094688235

IUPAC Name

1,5,8,11-tetrahydroxy-3-methyl-1,2,3,4,7,12-hexahydrotetraphene-7,12-dione

Traditional Name

1,5,8,11-tetrahydroxy-3-methyl-1,2,3,4-tetrahydrotetraphene-7,12-dione

CAS Registry Number

Not Available

SMILES

CC1CC(O)C2=C3C(=O)C4=C(O)C=CC(O)=C4C(=O)C3=CC(O)=C2C1

InChI Identifier

InChI=1S/C19H16O6/c1-7-4-8-12(22)6-9-15(14(8)13(23)5-7)19(25)17-11(21)3-2-10(20)16(17)18(9)24/h2-3,6-7,13,20-23H,4-5H2,1H3

InChI Key

NXMMIDHKNNDZHM-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as angucyclines. These are polyketides with a structure based on then benz[a]anthracene skeleton, with the particularity that the central ring of the anthracene moiety is a para-quinone.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Angucyclines

Sub Class

Not Available

Direct Parent

Angucyclines

Alternative Parents

Substituents

Angucycline core
Hydroxyanthraquinone
Anthraquinone
9,10-anthraquinone
Phenanthrol
Phenanthrene
Anthracene
Tetralin
Aryl ketone
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Vinylogous acid
Secondary alcohol
Ketone
Polyol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.25 g/L	ALOGPS
logP	2.36	ALOGPS
logP	3.82	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	7.4	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	115.06 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	90.64 m³·mol⁻¹	ChemAxon
Polarizability	34.55 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

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/Eubacteria	Actinobacteria	1		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

78435061

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139587902

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 Hatomarubigin F (MMDBc0017430)

MOL for #<Metabolite:0x00007f8dc599a520>

3D MOL for #<Metabolite:0x00007f8dc599a520>

3D SDF for #<Metabolite:0x00007f8dc599a520>

3D-SDF for #<Metabolite:0x00007f8dc599a520>

PDB for #<Metabolite:0x00007f8dc599a520>

3D PDB for #<Metabolite:0x00007f8dc599a520>

SMILES for #<Metabolite:0x00007f8dc599a520>

INCHI for #<Metabolite:0x00007f8dc599a520>

Structure for #<Metabolite:0x00007f8dc599a520>

3D Structure for #<Metabolite:0x00007f8dc599a520>