MiMeDB: Showing metabocard for Clostrubin A (MMDBc0006369)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-14 23:36:44 UTC

Update Date

2025-10-07 16:05:08 UTC

Metabolite ID

MMDBc0006369

Metabolite Identification

Common Name

Clostrubin A

Description

Clostrubin A is a pentacyclic natural product belonging to the class of metabolites. It is characterized by its complex chemical structure, which is integral to its biological activity. Notably, the accomplished pentacyclic structures constitute the complete core structures of natural products, namely clostrubin and borolithochromes, offering a rapid synthetic route (PMID:40586692 ). This highlights the significance of Clostrubin A in the context of synthetic organic chemistry and natural product synthesis. In practical applications, a notable quantity of 200 mg of clostrubin can be delivered through this synthetic approach, emphasizing its potential utility in various research and therapeutic contexts (PMID:25759087 ). The study of Clostrubin A not only contributes to our understanding of complex natural products but also opens avenues for exploring its biological implications and potential applications in medicine.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152101362D          

 31 35  0  0  0  0            999 V2000
    3.6062    1.3284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    5.0702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5246    0.8607    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
   -0.9845    3.6671    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
    3.8763    2.7316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6358    5.5380    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3362    2.1079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0957    4.9143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7946    1.6402    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
   -0.1744    3.5111    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
    3.6062    3.5111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4459    5.3821    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
    2.7961    3.6671    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
    0.0957    2.7316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7159    4.6025    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
   -0.4444    2.1079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5261    4.4466    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
   -2.6048    1.7961    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1463    4.1348    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9860    6.0057    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1744    1.3284    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0662    5.0702    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
  5  4  2  0  0  0  0
  9  1  1  0  0  0  0
  9  6  1  0  0  0  0
  9  7  2  0  0  0  0
 10  2  1  0  0  0  0
 10  8  2  0  0  0  0
 11  3  1  4  0  0  0
 12  4  1  0  0  0  0
 12 11  2  0  0  0  0
 13  5  1  0  0  0  0
 14  6  2  0  0  0  0
 15  7  1  0  0  0  0
 16  8  1  0  0  0  0
 17 10  1  0  0  0  0
 17 13  2  0  0  0  0
 18 14  1  0  0  0  0
 18 15  1  0  0  0  0
 19 14  1  0  0  0  0
 20 13  1  0  0  0  0
 21 16  2  0  0  0  0
 22 17  1  0  0  0  0
 22 19  2  0  0  0  0
 22 21  1  0  0  0  0
 23 12  1  0  0  0  0
 23 20  2  0  0  0  0
 24 18  2  0  0  0  0
 24 21  1  0  0  0  0
 25 19  1  0  0  0  0
 25 20  1  0  0  0  0
 26 11  1  0  0  0  0
 27 15  2  0  0  0  0
 28 16  1  0  0  0  0
 29 23  1  0  0  0  0
 30 24  1  0  0  0  0
 31 25  2  0  0  0  0
M  END


  Mrv1652305152101362D          

 31 35  0  0  0  0            999 V2000
    3.6062    1.3284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    5.0702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5246    0.8607    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
   -0.9845    3.6671    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
    3.8763    2.7316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6358    5.5380    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3362    2.1079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0957    4.9143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7946    1.6402    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
   -0.1744    3.5111    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
    3.6062    3.5111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4459    5.3821    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
    2.7961    3.6671    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
    0.0957    2.7316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7159    4.6025    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
   -0.4444    2.1079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5261    4.4466    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
   -2.6048    1.7961    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1463    4.1348    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9860    6.0057    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1744    1.3284    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0662    5.0702    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
  5  4  2  0  0  0  0
  9  1  1  0  0  0  0
  9  6  1  0  0  0  0
  9  7  2  0  0  0  0
 10  2  1  0  0  0  0
 10  8  2  0  0  0  0
 11  3  1  4  0  0  0
 12  4  1  0  0  0  0
 12 11  2  0  0  0  0
 13  5  1  0  0  0  0
 14  6  2  0  0  0  0
 15  7  1  0  0  0  0
 16  8  1  0  0  0  0
 17 10  1  0  0  0  0
 17 13  2  0  0  0  0
 18 14  1  0  0  0  0
 18 15  1  0  0  0  0
 19 14  1  0  0  0  0
 20 13  1  0  0  0  0
 21 16  2  0  0  0  0
 22 17  1  0  0  0  0
 22 19  2  0  0  0  0
 22 21  1  0  0  0  0
 23 12  1  0  0  0  0
 23 20  2  0  0  0  0
 24 18  2  0  0  0  0
 24 21  1  0  0  0  0
 25 19  1  0  0  0  0
 25 20  1  0  0  0  0
 26 11  1  0  0  0  0
 27 15  2  0  0  0  0
 28 16  1  0  0  0  0
 29 23  1  0  0  0  0
 30 24  1  0  0  0  0
 31 25  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0006369

> <DATABASE_NAME>
MIME

> <SMILES>
CC(O)=C1C=CC2=C3C(C)=CC(O)=C4C(O)=C5C(=O)C=C(C)C=C5C(C(=O)C2=C1O)=C34

> <INCHI_IDENTIFIER>
InChI=1S/C25H18O6/c1-9-6-14-18(15(27)7-9)24(30)21-16(28)8-10(2)17-13-5-4-12(11(3)26)23(29)20(13)25(31)19(14)22(17)21/h4-8,26,28-30H,1-3H3

> <INCHI_KEY>
HKZBCPLWGPITMW-UHFFFAOYSA-N

> <FORMULA>
C25H18O6

> <MOLECULAR_WEIGHT>
414.413

> <EXACT_MASS>
414.1103383

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
43.55046003056161

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
8,10,18-trihydroxy-17-(1-hydroxyethylidene)-4,12-dimethylpentacyclo[11.7.1.0^{2,7}.0^{9,21}.0^{14,19}]henicosa-1(21),2,4,7,9,11,13,15,18-nonaene-6,20-dione

> <ALOGPS_LOGP>
1.37

> <JCHEM_LOGP>
0.12601245600000055

> <ALOGPS_LOGS>
-4.78

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.125442381092384

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.273441960614514

> <JCHEM_PKA_STRONGEST_BASIC>
3.6558885397722283

> <JCHEM_POLAR_SURFACE_AREA>
115.06

> <JCHEM_REFRACTIVITY>
124.68829999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.88e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
8,10,18-trihydroxy-17-(1-hydroxyethylidene)-4,12-dimethylpentacyclo[11.7.1.0^{2,7}.0^{9,21}.0^{14,19}]henicosa-1(21),2,4,7,9,11,13,15,18-nonaene-6,20-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       6.732   2.480   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334   9.464   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.846   1.607   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.846   5.681   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.838   6.845   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.715   4.226   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.236   5.099   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.187  10.338   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.228   3.935   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.179   9.173   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.350   3.062   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.342   4.226   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.326   6.554   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.211   5.681   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.732   6.554   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.699  10.047   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.683   7.718   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.219   6.845   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.699   5.972   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.179   5.099   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.203   8.591   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.195   7.427   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.830   3.935   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.715   8.300   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.691   4.808   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -4.862   3.353   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       7.740   7.718   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       3.707  11.211   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -0.326   2.480   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       5.723   9.464   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       2.195   3.353   0.000  0.00  0.00           O+0
CONECT    1    9                                                            
CONECT    2   10                                                            
CONECT    3   11                                                            
CONECT    4    5   12                                                       
CONECT    5    4   13                                                       
CONECT    6    9   14                                                       
CONECT    7    9   15                                                       
CONECT    8   10   16                                                       
CONECT    9    1    6    7                                                  
CONECT   10    2    8   17                                                  
CONECT   11    3   12   26                                                  
CONECT   12    4   11   23                                                  
CONECT   13    5   17   20                                                  
CONECT   14    6   18   19                                                  
CONECT   15    7   18   27                                                  
CONECT   16    8   21   28                                                  
CONECT   17   10   13   22                                                  
CONECT   18   14   15   24                                                  
CONECT   19   14   22   25                                                  
CONECT   20   13   23   25                                                  
CONECT   21   16   22   24                                                  
CONECT   22   17   19   21                                                  
CONECT   23   12   20   29                                                  
CONECT   24   18   21   30                                                  
CONECT   25   19   20   31                                                  
CONECT   26   11                                                            
CONECT   27   15                                                            
CONECT   28   16                                                            
CONECT   29   23                                                            
CONECT   30   24                                                            
CONECT   31   25                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   70    0
END

Synonyms

Value	Source
Clostrubin	MeSH

Molecular Formula

C₂₅H₁₈O₆

Average Mass

414.413

Monoisotopic Mass

414.1103383

IUPAC Name

8,10,18-trihydroxy-17-(1-hydroxyethylidene)-4,12-dimethylpentacyclo[11.7.1.0^{2,7}.0^{9,21}.0^{14,19}]henicosa-1(21),2,4,7,9,11,13,15,18-nonaene-6,20-dione

Traditional Name

8,10,18-trihydroxy-17-(1-hydroxyethylidene)-4,12-dimethylpentacyclo[11.7.1.0^{2,7}.0^{9,21}.0^{14,19}]henicosa-1(21),2,4,7,9,11,13,15,18-nonaene-6,20-dione

CAS Registry Number

Not Available

SMILES

CC(O)=C1C=CC2=C3C(C)=CC(O)=C4C(O)=C5C(=O)C=C(C)C=C5C(C(=O)C2=C1O)=C34

InChI Identifier

InChI=1S/C25H18O6/c1-9-6-14-18(15(27)7-9)24(30)21-16(28)8-10(2)17-13-5-4-12(11(3)26)23(29)20(13)25(31)19(14)22(17)21/h4-8,26,28-30H,1-3H3

InChI Key

HKZBCPLWGPITMW-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenanthrols. Phenanthrols are compounds containing a phenanthrene (or its hydrogenated derivative) to which a hydroxyl group is attached.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Phenanthrenes and derivatives

Sub Class

Phenanthrols

Direct Parent

Phenanthrols

Alternative Parents

Substituents

Phenanthrol
Anthracene
1-naphthol
2-naphthol
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Vinylogous acid
Ketone
Polyol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
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	0.0069 g/L	ALOGPS
logP	1.37	ALOGPS
logP	0.13	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	6.27	ChemAxon
pKa (Strongest Basic)	3.66	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	115.06 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	124.69 m³·mol⁻¹	ChemAxon
Polarizability	43.55 Å³	ChemAxon
Number of Rings	5	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/Eubacteria	Firmicutes	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

78434736

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

136744537

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 Clostrubin A (MMDBc0006369)

MOL for #<Metabolite:0x00007fb4ca1b8b28>

3D MOL for #<Metabolite:0x00007fb4ca1b8b28>

3D SDF for #<Metabolite:0x00007fb4ca1b8b28>

3D-SDF for #<Metabolite:0x00007fb4ca1b8b28>

PDB for #<Metabolite:0x00007fb4ca1b8b28>

3D PDB for #<Metabolite:0x00007fb4ca1b8b28>

SMILES for #<Metabolite:0x00007fb4ca1b8b28>

INCHI for #<Metabolite:0x00007fb4ca1b8b28>

Structure for #<Metabolite:0x00007fb4ca1b8b28>

3D Structure for #<Metabolite:0x00007fb4ca1b8b28>