MiMeDB: Showing metabocard for Gramilaurone (MMDBc0019037)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 09:09:47 UTC

Update Date

2022-08-31 06:44:50 UTC

Metabolite ID

MMDBc0019037

Metabolite Identification

Common Name

Gramilaurone

Description

4,12,13-trihydroxy-9-(hydroxymethyl)-6,10-dimethyl-3,14-dioxatetracyclo[6.5.1.0¹,¹⁰.0⁴,⁹]tetradecan-5-one belongs to the class of organic compounds known as 1,4-dioxepanes. These are dioxepanes with the two ring oxygen atoms at position 1 and 4, respectively. 4,12,13-trihydroxy-9-(hydroxymethyl)-6,10-dimethyl-3,14-dioxatetracyclo[6.5.1.0¹,¹⁰.0⁴,⁹]tetradecan-5-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004201503312D          

 22 25  0  0  0  0            999 V2000
    4.2124    1.7192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2262    1.5383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1223    0.6723    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3954    0.2246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5861   -0.1433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0400    0.5032    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4600    1.1221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8735    1.8703    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8029    1.7776    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8088    2.7100    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5572    2.0523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7240    2.9657    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1260    0.9017    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0674    1.1373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9253    0.7786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6137    1.0961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4161    1.5451    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2271    1.8249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4145    1.6825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3670    2.1751    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2988    0.8657    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3274    0.2466    0.0000 O   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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  2 11  1  0  0  0  0
 11 12  2  0  0  0  0
  9 13  1  0  0  0  0
  4 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 13 16  1  0  0  0  0
  6 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
  6 21  1  0  0  0  0
 21 22  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0019037

> <DATABASE_NAME>
MIME

> <SMILES>
CC1CC2OC34COC(O)(C1=O)C2(CO)C3(C)CC(O)C4O

> <INCHI_IDENTIFIER>
InChI=1S/C15H22O7/c1-7-3-9-13(5-16)12(2)4-8(17)11(19)14(12,22-9)6-21-15(13,20)10(7)18/h7-9,11,16-17,19-20H,3-6H2,1-2H3

> <INCHI_KEY>
TYSOJSRFFIKNBS-UHFFFAOYSA-N

> <FORMULA>
C15H22O7

> <MOLECULAR_WEIGHT>
314.334

> <EXACT_MASS>
314.136553048

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
30.84838472120431

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,12,13-trihydroxy-9-(hydroxymethyl)-6,10-dimethyl-3,14-dioxatetracyclo[6.5.1.0¹,¹⁰.0⁴,⁹]tetradecan-5-one

> <ALOGPS_LOGP>
-1.00

> <JCHEM_LOGP>
-1.012486875

> <ALOGPS_LOGS>
-0.67

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.93955084215806

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.823917489369746

> <JCHEM_PKA_STRONGEST_BASIC>
-2.874792569456239

> <JCHEM_POLAR_SURFACE_AREA>
116.45

> <JCHEM_REFRACTIVITY>
72.44109999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.78e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,12,13-trihydroxy-9-(hydroxymethyl)-6,10-dimethyl-3,14-dioxatetracyclo[6.5.1.0¹,¹⁰.0⁴,⁹]tetradecan-5-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-15         0                                  
HETATM    1  C   UNK     0       7.863   3.209   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.022   2.872   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.828   1.255   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.471   0.419   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.961  -0.268   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.941   0.939   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.859   2.095   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.630   3.491   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       3.365   3.318   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       3.376   5.059   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.773   3.831   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.085   5.536   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       3.969   1.683   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.726   2.123   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       7.327   1.453   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       3.012   2.046   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.510   2.884   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.291   3.407   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.774   3.141   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.685   4.060   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.558   1.616   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -0.611   0.460   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   13                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   16   21                                             
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11   13                                             
CONECT   10    9                                                            
CONECT   11    9    2   12                                                  
CONECT   12   11                                                            
CONECT   13    9    4   14   16                                             
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   13    6   17   18                                             
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19    6   22                                                  
CONECT   22   21                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   50    0
END

Synonyms

Not Available

Molecular Formula

C₁₅H₂₂O₇

Average Mass

314.334

Monoisotopic Mass

314.136553048

IUPAC Name

4,12,13-trihydroxy-9-(hydroxymethyl)-6,10-dimethyl-3,14-dioxatetracyclo[6.5.1.0¹,¹⁰.0⁴,⁹]tetradecan-5-one

Traditional Name

4,12,13-trihydroxy-9-(hydroxymethyl)-6,10-dimethyl-3,14-dioxatetracyclo[6.5.1.0¹,¹⁰.0⁴,⁹]tetradecan-5-one

CAS Registry Number

Not Available

SMILES

CC1CC2OC34COC(O)(C1=O)C2(CO)C3(C)CC(O)C4O

InChI Identifier

InChI=1S/C15H22O7/c1-7-3-9-13(5-16)12(2)4-8(17)11(19)14(12,22-9)6-21-15(13,20)10(7)18/h7-9,11,16-17,19-20H,3-6H2,1-2H3

InChI Key

TYSOJSRFFIKNBS-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,4-dioxepanes. These are dioxepanes with the two ring oxygen atoms at position 1 and 4, respectively.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Dioxepanes

Sub Class

1,4-dioxepanes

Direct Parent

1,4-dioxepanes

Alternative Parents

Substituents

1,4-dioxepane
Oxane
Cyclic alcohol
Tetrahydrofuran
Hemiacetal
Ketone
Secondary alcohol
Polyol
Ether
Dialkyl ether
Oxacycle
Hydrocarbon derivative
Organooxygen compound
Alcohol
Organic oxygen compound
Organic oxide
Carbonyl group
Primary alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	67.8 g/L	ALOGPS
logP	-1	ALOGPS
logP	-1	ChemAxon
logS	-0.67	ALOGPS
pKa (Strongest Acidic)	9.82	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	116.45 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	72.44 m³·mol⁻¹	ChemAxon
Polarizability	30.85 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

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	Ascomycota	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

73817727

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 Gramilaurone (MMDBc0019037)

MOL for #<Metabolite:0x00007f92340ac2b0>

3D MOL for #<Metabolite:0x00007f92340ac2b0>

3D SDF for #<Metabolite:0x00007f92340ac2b0>

3D-SDF for #<Metabolite:0x00007f92340ac2b0>

PDB for #<Metabolite:0x00007f92340ac2b0>

3D PDB for #<Metabolite:0x00007f92340ac2b0>

SMILES for #<Metabolite:0x00007f92340ac2b0>

INCHI for #<Metabolite:0x00007f92340ac2b0>

Structure for #<Metabolite:0x00007f92340ac2b0>

3D Structure for #<Metabolite:0x00007f92340ac2b0>