MiMeDB: Showing metabocard for Yicathin C (MMDBc0005321)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-14 22:57:17 UTC

Update Date

2022-08-31 06:23:41 UTC

Metabolite ID

MMDBc0005321

Metabolite Identification

Common Name

Yicathin C

Description

Yicathin C belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring. Yicathin C is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152100572D          

 22 24  0  0  0  0            999 V2000
    5.7158    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  7  1  1  0  0  0  0
  7  3  2  0  0  0  0
  7  4  1  0  0  0  0
  8  5  2  0  0  0  0
  8  6  1  0  0  0  0
  9  3  1  0  0  0  0
 10  5  1  0  0  0  0
 11  4  2  0  0  0  0
 12  6  2  0  0  0  0
 13  9  2  0  0  0  0
 13 11  1  0  0  0  0
 14 10  2  0  0  0  0
 14 12  1  0  0  0  0
 15 13  1  0  0  0  0
 15 14  1  0  0  0  0
 16  8  1  0  0  0  0
 17  9  1  0  0  0  0
 18 15  2  0  0  0  0
 19 16  2  0  0  0  0
 20 16  1  0  0  0  0
 21  2  1  0  0  0  0
 21 10  1  0  0  0  0
 22 11  1  0  0  0  0
 22 12  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0005321

> <DATABASE_NAME>
MIME

> <SMILES>
COC1=C2C(=O)C3=C(O)C=C(C)C=C3OC2=CC(=C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H12O6/c1-7-3-9(17)13-11(4-7)22-12-6-8(16(19)20)5-10(21-2)14(12)15(13)18/h3-6,17H,1-2H3,(H,19,20)

> <INCHI_KEY>
CDOFUOUENPZVAF-UHFFFAOYSA-N

> <FORMULA>
C16H12O6

> <MOLECULAR_WEIGHT>
300.266

> <EXACT_MASS>
300.063388106

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
29.835882851734276

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
8-hydroxy-1-methoxy-6-methyl-9-oxo-9H-xanthene-3-carboxylic acid

> <ALOGPS_LOGP>
2.45

> <JCHEM_LOGP>
3.319407930333333

> <ALOGPS_LOGS>
-3.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.487877679392891

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3242625859973742

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7439707093141954

> <JCHEM_POLAR_SURFACE_AREA>
93.06000000000002

> <JCHEM_REFRACTIVITY>
77.55779999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.85e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
8-hydroxy-1-methoxy-6-methyl-9-oxoxanthene-3-carboxylic acid

> <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      10.669   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       8.002   6.160   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       5.335   6.160   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000  -0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
CONECT    1    7                                                            
CONECT    2   21                                                            
CONECT    3    7    9                                                       
CONECT    4    7   11                                                       
CONECT    5    8   10                                                       
CONECT    6    8   12                                                       
CONECT    7    1    3    4                                                  
CONECT    8    5    6   16                                                  
CONECT    9    3   13   17                                                  
CONECT   10    5   14   21                                                  
CONECT   11    4   13   22                                                  
CONECT   12    6   14   22                                                  
CONECT   13    9   11   15                                                  
CONECT   14   10   12   15                                                  
CONECT   15   13   14   18                                                  
CONECT   16    8   19   20                                                  
CONECT   17    9                                                            
CONECT   18   15                                                            
CONECT   19   16                                                            
CONECT   20   16                                                            
CONECT   21    2   10                                                       
CONECT   22   11   12                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

Synonyms

Not Available

Molecular Formula

C₁₆H₁₂O₆

Average Mass

300.266

Monoisotopic Mass

300.063388106

IUPAC Name

8-hydroxy-1-methoxy-6-methyl-9-oxo-9H-xanthene-3-carboxylic acid

Traditional Name

8-hydroxy-1-methoxy-6-methyl-9-oxoxanthene-3-carboxylic acid

CAS Registry Number

Not Available

SMILES

COC1=C2C(=O)C3=C(O)C=C(C)C=C3OC2=CC(=C1)C(O)=O

InChI Identifier

InChI=1S/C16H12O6/c1-7-3-9(17)13-11(4-7)22-12-6-8(16(19)20)5-10(21-2)14(12)15(13)18/h3-6,17H,1-2H3,(H,19,20)

InChI Key

CDOFUOUENPZVAF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Xanthones

Alternative Parents

Substituents

Xanthone
Chromone
M-methoxybenzoic acid or derivatives
Anisole
Phenol ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Pyranone
Benzenoid
Pyran
Heteroaromatic compound
Vinylogous ester
Vinylogous acid
Ether
Carboxylic acid
Carboxylic acid derivative
Oxacycle
Organooxygen compound
Organic oxygen 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	0.068 g/L	ALOGPS
logP	2.45	ALOGPS
logP	3.32	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	3.32	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	93.06 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	77.56 m³·mol⁻¹	ChemAxon
Polarizability	29.84 Å³	ChemAxon
Number of Rings	3	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	1	Human	Metabolic reconstruction

Exposure Sources

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

30770923

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

102191487

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 Yicathin C (MMDBc0005321)

MOL for #<Metabolite:0x00007fdb4000d1b0>

3D MOL for #<Metabolite:0x00007fdb4000d1b0>

3D SDF for #<Metabolite:0x00007fdb4000d1b0>

3D-SDF for #<Metabolite:0x00007fdb4000d1b0>

PDB for #<Metabolite:0x00007fdb4000d1b0>

3D PDB for #<Metabolite:0x00007fdb4000d1b0>

SMILES for #<Metabolite:0x00007fdb4000d1b0>

INCHI for #<Metabolite:0x00007fdb4000d1b0>

Structure for #<Metabolite:0x00007fdb4000d1b0>

3D Structure for #<Metabolite:0x00007fdb4000d1b0>