MiMeDB: Showing metabocard for Sterin A (MMDBc0020041)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 10:01:12 UTC

Update Date

2022-08-31 06:46:21 UTC

Metabolite ID

MMDBc0020041

Metabolite Identification

Common Name

Sterin A

Description

2-[(2,2-dimethyl-2H-chromen-6-yl)oxy]-5-(hydroxymethyl)oxolane-3,4-diol belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. 2-[(2,2-dimethyl-2H-chromen-6-yl)oxy]-5-(hydroxymethyl)oxolane-3,4-diol is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004191514502D          

 22 24  0  0  0  0            999 V2000
    0.4323    0.3627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0980   -0.5558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    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
    4.2868   -1.6500    0.0000 O   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
    4.9543   -2.9599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6993   -3.7445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1842   -4.4120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0047   -4.3257    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8743   -3.7445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3894   -4.4120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6194   -2.9599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8348   -2.7050    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    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
    1.4289   -1.6500    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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 10 17  1  0  0  0  0
 17 18  1  0  0  0  0
  8 19  1  0  0  0  0
 19 20  2  0  0  0  0
  5 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
  2 22  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0020041

> <DATABASE_NAME>
MIME

> <SMILES>
CC1(C)OC2=CC=C(OC3OC(CO)C(O)C3O)C=C2C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C16H20O6/c1-16(2)6-5-9-7-10(3-4-11(9)22-16)20-15-14(19)13(18)12(8-17)21-15/h3-7,12-15,17-19H,8H2,1-2H3

> <INCHI_KEY>
VWBXKUAVNIEMKH-UHFFFAOYSA-N

> <FORMULA>
C16H20O6

> <MOLECULAR_WEIGHT>
308.33

> <EXACT_MASS>
308.125988364

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
31.748103821413252

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(2,2-dimethyl-2H-chromen-6-yl)oxy]-5-(hydroxymethyl)oxolane-3,4-diol

> <ALOGPS_LOGP>
1.23

> <JCHEM_LOGP>
0.9325707450000005

> <ALOGPS_LOGS>
-2.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.825892168300943

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.264792608932593

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9811523889017764

> <JCHEM_POLAR_SURFACE_AREA>
88.38000000000001

> <JCHEM_REFRACTIVITY>
78.6142

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.89e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[(2,2-dimethylchromen-6-yl)oxy]-5-(hydroxymethyl)oxolane-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  C   UNK     0       0.807   0.677   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.183  -1.037   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       9.248  -5.525   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       8.772  -6.990   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.677  -8.236   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      11.209  -8.075   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       7.232  -6.990   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.327  -8.236   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       6.756  -5.525   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.292  -5.049   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4   22                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   20                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   19                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   17                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   10   18                                                  
CONECT   18   17                                                            
CONECT   19    8   20                                                       
CONECT   20   19    5   21                                                  
CONECT   21   20   22                                                       
CONECT   22   21    2                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

Synonyms

Not Available

Molecular Formula

C₁₆H₂₀O₆

Average Mass

308.33

Monoisotopic Mass

308.125988364

IUPAC Name

2-[(2,2-dimethyl-2H-chromen-6-yl)oxy]-5-(hydroxymethyl)oxolane-3,4-diol

Traditional Name

2-[(2,2-dimethylchromen-6-yl)oxy]-5-(hydroxymethyl)oxolane-3,4-diol

CAS Registry Number

Not Available

SMILES

CC1(C)OC2=CC=C(OC3OC(CO)C(O)C3O)C=C2C=C1

InChI Identifier

InChI=1S/C16H20O6/c1-16(2)6-5-9-7-10(3-4-11(9)22-16)20-15-14(19)13(18)12(8-17)21-15/h3-7,12-15,17-19H,8H2,1-2H3

InChI Key

VWBXKUAVNIEMKH-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Phenolic glycosides

Alternative Parents

Substituents

Phenolic glycoside
2,2-dimethyl-1-benzopyran
O-glycosyl compound
Benzopyran
Pentose monosaccharide
1-benzopyran
Alkyl aryl ether
Monosaccharide
Benzenoid
Oxolane
Secondary alcohol
Ether
Acetal
Oxacycle
Organoheterocyclic compound
Primary alcohol
Alcohol
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	2.89 g/L	ALOGPS
logP	1.23	ALOGPS
logP	0.93	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	12.26	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	88.38 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	78.61 m³·mol⁻¹	ChemAxon
Polarizability	31.75 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

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
Eukaryota/Fungi	Basidiomycota	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101163640

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 Sterin A (MMDBc0020041)

MOL for #<Metabolite:0x0000560be21d1fe8>

3D MOL for #<Metabolite:0x0000560be21d1fe8>

3D SDF for #<Metabolite:0x0000560be21d1fe8>

3D-SDF for #<Metabolite:0x0000560be21d1fe8>

PDB for #<Metabolite:0x0000560be21d1fe8>

3D PDB for #<Metabolite:0x0000560be21d1fe8>

SMILES for #<Metabolite:0x0000560be21d1fe8>

INCHI for #<Metabolite:0x0000560be21d1fe8>

Structure for #<Metabolite:0x0000560be21d1fe8>

3D Structure for #<Metabolite:0x0000560be21d1fe8>