MiMeDB: Showing metabocard for Dehydrorabelomycin (MMDBc0020347)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 10:21:04 UTC

Update Date

2022-08-31 06:46:37 UTC

Metabolite ID

MMDBc0020347

Metabolite Identification

Common Name

Dehydrorabelomycin

Description

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

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004151519342D          

 24 27  0  0  0  0            999 V2000
   -0.1913   -2.9882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188   -3.1441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589   -2.5204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9690   -2.6764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5091   -2.0527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2391   -3.4559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0492   -3.6118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5893   -2.9882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3193   -2.2086    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3994   -3.1441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9395   -2.5204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7497   -2.6764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0197   -3.4559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4796   -4.0796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7497   -4.8591    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6695   -3.9236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1294   -4.5473    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3994   -5.3268    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3193   -4.3914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7792   -5.0150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0492   -5.7946    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9690   -4.8591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990   -4.0796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8889   -3.9236    0.0000 C   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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 10 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
  7 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
 22 23  1  0  0  0  0
  6 23  1  0  0  0  0
 23 24  2  0  0  0  0
  2 24  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0020347

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=CC(O)=C2C(=C1)C=C(O)C1=C2C(=O)C2=CC=CC(O)=C2C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C19H12O5/c1-8-5-9-7-13(22)16-17(14(9)12(21)6-8)18(23)10-3-2-4-11(20)15(10)19(16)24/h2-7,20-22H,1H3

> <INCHI_KEY>
PQVIKROZFPIERS-UHFFFAOYSA-N

> <FORMULA>
C19H12O5

> <MOLECULAR_WEIGHT>
320.3

> <EXACT_MASS>
320.068473486

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
32.42322899588488

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1,6,8-trihydroxy-3-methyl-7,12-dihydrotetraphene-7,12-dione

> <ALOGPS_LOGP>
3.19

> <JCHEM_LOGP>
4.810908255666666

> <ALOGPS_LOGS>
-4.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.369236327701124

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.7225801467254875

> <JCHEM_PKA_STRONGEST_BASIC>
-5.646927005622275

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
88.5851

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.94e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dehydrorabelomycin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-APR-15         0                                  
HETATM    1  C   UNK     0      -0.357  -5.578   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.155  -5.869   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.163  -4.705   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.676  -4.996   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.684  -3.832   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.180  -6.451   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.692  -6.742   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.700  -5.578   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.196  -4.123   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       8.212  -5.869   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.220  -4.705   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.733  -4.996   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      11.237  -6.451   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.229  -7.615   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      10.733  -9.070   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       8.716  -7.324   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.708  -8.488   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       8.212  -9.943   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       6.196  -8.197   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.188  -9.361   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       5.692 -10.817   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       3.676  -9.070   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.171  -7.615   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.659  -7.324   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   24                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   23                                                  
CONECT    7    6    8   19                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   16                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   10   17                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17    7   20                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22    6   24                                                  
CONECT   24   23    2                                                       
MASTER        0    0    0    0    0    0    0    0   24    0   54    0
END

Synonyms

Not Available

Molecular Formula

C₁₉H₁₂O₅

Average Mass

320.3

Monoisotopic Mass

320.068473486

IUPAC Name

1,6,8-trihydroxy-3-methyl-7,12-dihydrotetraphene-7,12-dione

Traditional Name

dehydrorabelomycin

CAS Registry Number

Not Available

SMILES

CC1=CC(O)=C2C(=C1)C=C(O)C1=C2C(=O)C2=CC=CC(O)=C2C1=O

InChI Identifier

InChI=1S/C19H12O5/c1-8-5-9-7-13(22)16-17(14(9)12(21)6-8)18(23)10-3-2-4-11(20)15(10)19(16)24/h2-7,20-22H,1H3

InChI Key

PQVIKROZFPIERS-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
9,10-anthraquinone
Anthraquinone
Phenanthrol
Anthracene
Phenanthrene
2-naphthol
1-naphthol
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Vinylogous acid
Ketone
Polyol
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

angucycline (CHEBI:31461 )
an angucyclin (CPD-12952 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.029 g/L	ALOGPS
logP	3.19	ALOGPS
logP	4.81	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	7.72	ChemAxon
pKa (Strongest Basic)	-5.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	88.59 m³·mol⁻¹	ChemAxon
Polarizability	32.42 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	3	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

C00015999

Chemspider ID

Not Available

KEGG Compound ID

C12390

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

443801

PDB ID

Not Available

ChEBI ID

31461

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 Dehydrorabelomycin (MMDBc0020347)

MOL for #<Metabolite:0x00007fece8f49d18>

3D MOL for #<Metabolite:0x00007fece8f49d18>

3D SDF for #<Metabolite:0x00007fece8f49d18>

3D-SDF for #<Metabolite:0x00007fece8f49d18>

PDB for #<Metabolite:0x00007fece8f49d18>

3D PDB for #<Metabolite:0x00007fece8f49d18>

SMILES for #<Metabolite:0x00007fece8f49d18>

INCHI for #<Metabolite:0x00007fece8f49d18>

Structure for #<Metabolite:0x00007fece8f49d18>

3D Structure for #<Metabolite:0x00007fece8f49d18>