MiMeDB: Showing metabocard for Sorokinianin (MMDBc0004761)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-14 22:37:07 UTC

Update Date

2022-08-31 06:22:56 UTC

Metabolite ID

MMDBc0004761

Metabolite Identification

Common Name

Sorokinianin

Description

(3R,5S)-3-hydroxy-5-[(1R,4R,5S,8S)-8-(hydroxymethyl)-1-methyl-7-methylidene-4-(propan-2-yl)bicyclo[3.2.1]octan-6-yl]oxolan-2-one belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring. Based on a literature review very few articles have been published on (3R,5S)-3-hydroxy-5-[(1R,4R,5S,8S)-8-(hydroxymethyl)-1-methyl-7-methylidene-4-(propan-2-yl)bicyclo[3.2.1]octan-6-yl]oxolan-2-one.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152100372D          

 28 30  0  0  1  0            999 V2000
    3.4102    2.1808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2930    3.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1126    0.1450    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0921   -0.8157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4380    0.9155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0800    0.1722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2599    2.4977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2190    0.9155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5944    2.3038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6307    0.5030    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0800    1.6588    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0440    0.9155    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0774    2.6084    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1126    1.6859    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6307    1.3280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2757    1.8423    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4354    1.8651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2757   -0.0114    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3941    0.3634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4684    3.3349    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2471    1.7178    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8391    1.2950    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8075    2.4375    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8690    0.9155    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9022    2.5899    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5438    2.1857    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1826    1.1894    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1107    2.6507    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  9  1  1  0  0  0  0
  9  2  1  0  0  0  0
 10  3  2  0  0  0  0
 11  5  1  0  0  0  0
 11  9  1  1  0  0  0
 12  8  1  0  0  0  0
 13  7  1  0  0  0  0
 14  7  1  0  0  0  0
 15 10  1  0  0  0  0
 14 15  1  1  0  0  0
 16 11  1  0  0  0  0
 16 12  1  0  0  0  0
 16 15  1  0  0  0  0
 17 13  1  0  0  0  0
 18  4  1  6  0  0  0
 18  6  1  0  0  0  0
 18 10  1  0  0  0  0
 18 12  1  0  0  0  0
 19  8  1  0  0  0  0
 13 20  1  6  0  0  0
 21 17  2  0  0  0  0
 22 14  1  0  0  0  0
 22 17  1  0  0  0  0
 11 23  1  6  0  0  0
 12 24  1  6  0  0  0
 13 25  1  1  0  0  0
 14 26  1  6  0  0  0
 27 15  1  0  0  0  0
 16 28  1  6  0  0  0
M  END


  Mrv1652305152100372D          

 28 30  0  0  1  0            999 V2000
    3.4102    2.1808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2930    3.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1126    0.1450    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0921   -0.8157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4380    0.9155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0800    0.1722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2599    2.4977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2190    0.9155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5944    2.3038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6307    0.5030    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0800    1.6588    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0440    0.9155    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0774    2.6084    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1126    1.6859    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6307    1.3280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2757    1.8423    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4354    1.8651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2757   -0.0114    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3941    0.3634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4684    3.3349    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2471    1.7178    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8391    1.2950    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8075    2.4375    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8690    0.9155    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9022    2.5899    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5438    2.1857    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1826    1.1894    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1107    2.6507    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  9  1  1  0  0  0  0
  9  2  1  0  0  0  0
 10  3  2  0  0  0  0
 11  5  1  0  0  0  0
 11  9  1  1  0  0  0
 12  8  1  0  0  0  0
 13  7  1  0  0  0  0
 14  7  1  0  0  0  0
 15 10  1  0  0  0  0
 14 15  1  1  0  0  0
 16 11  1  0  0  0  0
 16 12  1  0  0  0  0
 16 15  1  0  0  0  0
 17 13  1  0  0  0  0
 18  4  1  6  0  0  0
 18  6  1  0  0  0  0
 18 10  1  0  0  0  0
 18 12  1  0  0  0  0
 19  8  1  0  0  0  0
 13 20  1  6  0  0  0
 21 17  2  0  0  0  0
 22 14  1  0  0  0  0
 22 17  1  0  0  0  0
 11 23  1  6  0  0  0
 12 24  1  6  0  0  0
 13 25  1  1  0  0  0
 14 26  1  6  0  0  0
 27 15  1  0  0  0  0
 16 28  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0004761

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(O)C[C@]([H])(OC1=O)C1([H])C(=C)[C@]2(C)CC[C@]([H])(C(C)C)[C@@]1([H])[C@]2([H])CO

> <INCHI_IDENTIFIER>
InChI=1S/C18H28O4/c1-9(2)11-5-6-18(4)10(3)15(16(11)12(18)8-19)14-7-13(20)17(21)22-14/h9,11-16,19-20H,3,5-8H2,1-2,4H3/t11-,12+,13-,14+,15?,16+,18+/m1/s1

> <INCHI_KEY>
PTGFDIFCKGMAJK-HBBNERDWSA-N

> <FORMULA>
C18H28O4

> <MOLECULAR_WEIGHT>
308.418

> <EXACT_MASS>
308.198759382

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
34.41962268135778

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R,5S)-3-hydroxy-5-[(1R,4R,5S,8S)-8-(hydroxymethyl)-1-methyl-7-methylidene-4-(propan-2-yl)bicyclo[3.2.1]octan-6-yl]oxolan-2-one

> <ALOGPS_LOGP>
1.46

> <JCHEM_LOGP>
1.6763754800000006

> <ALOGPS_LOGS>
-2.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.65296108821207

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.619093140490563

> <JCHEM_PKA_STRONGEST_BASIC>
-1.20099454918955

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
83.36659999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.75e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,5S)-3-hydroxy-5-[(1R,4R,5S,8S)-8-(hydroxymethyl)-4-isopropyl-1-methyl-7-methylidenebicyclo[3.2.1]octan-6-yl]oxolan-2-one

> <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       6.366   4.071   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.280   5.734   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.210   0.271   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.039  -1.523   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.551   1.709   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.883   0.321   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.485   4.662   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.409   1.709   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.843   4.300   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.177   0.939   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.883   3.096   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.949   1.709   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.011   4.869   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.210   3.147   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.177   2.479   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.381   3.439   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.679   3.482   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.381  -0.021   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -0.736   0.678   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -2.741   6.225   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -4.195   3.207   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -1.566   2.417   0.000  0.00  0.00           O+0
HETATM   23  H   UNK     0       3.374   4.550   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       3.489   1.709   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0      -3.551   4.834   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       1.015   4.080   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0      -0.341   2.220   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0       2.073   4.948   0.000  0.00  0.00           H+0
CONECT    1    9                                                            
CONECT    2    9                                                            
CONECT    3   10                                                            
CONECT    4   18                                                            
CONECT    5    6   11                                                       
CONECT    6    5   18                                                       
CONECT    7   13   14                                                       
CONECT    8   12   19                                                       
CONECT    9    1    2   11                                                  
CONECT   10    3   15   18                                                  
CONECT   11    5    9   16   23                                             
CONECT   12    8   16   18   24                                             
CONECT   13    7   17   20   25                                             
CONECT   14    7   15   22   26                                             
CONECT   15   10   14   16   27                                             
CONECT   16   11   12   15   28                                             
CONECT   17   13   21   22                                                  
CONECT   18    4    6   10   12                                             
CONECT   19    8                                                            
CONECT   20   13                                                            
CONECT   21   17                                                            
CONECT   22   14   17                                                       
CONECT   23   11                                                            
CONECT   24   12                                                            
CONECT   25   13                                                            
CONECT   26   14                                                            
CONECT   27   15                                                            
CONECT   28   16                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   60    0
END

Synonyms

Not Available

Molecular Formula

C₁₈H₂₈O₄

Average Mass

308.418

Monoisotopic Mass

308.198759382

IUPAC Name

(3R,5S)-3-hydroxy-5-[(1R,4R,5S,8S)-8-(hydroxymethyl)-1-methyl-7-methylidene-4-(propan-2-yl)bicyclo[3.2.1]octan-6-yl]oxolan-2-one

Traditional Name

(3R,5S)-3-hydroxy-5-[(1R,4R,5S,8S)-8-(hydroxymethyl)-4-isopropyl-1-methyl-7-methylidenebicyclo[3.2.1]octan-6-yl]oxolan-2-one

CAS Registry Number

Not Available

SMILES

[H][C@@]1(O)C[C@]([H])(OC1=O)C1([H])C(=C)[C@]2(C)CC[C@]([H])(C(C)C)[C@@]1([H])[C@]2([H])CO

InChI Identifier

InChI=1S/C18H28O4/c1-9(2)11-5-6-18(4)10(3)15(16(11)12(18)8-19)14-7-13(20)17(21)22-14/h9,11-16,19-20H,3,5-8H2,1-2,4H3/t11-,12+,13-,14+,15?,16+,18+/m1/s1

InChI Key

PTGFDIFCKGMAJK-HBBNERDWSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Terpene lactones

Alternative Parents

Substituents

Terpene lactone
Sesquiterpenoid
Gamma butyrolactone
Tetrahydrofuran
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
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	0.38 g/L	ALOGPS
logP	1.46	ALOGPS
logP	1.68	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	12.62	ChemAxon
pKa (Strongest Basic)	-1.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	83.37 m³·mol⁻¹	ChemAxon
Polarizability	34.42 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
Eukaryota/Fungi	Ascomycota	1	Human feces	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

Not Available

Chemspider ID

23550609

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44715303

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 Sorokinianin (MMDBc0004761)

MOL for #<Metabolite:0x00007f46b6b84418>

3D MOL for #<Metabolite:0x00007f46b6b84418>

3D SDF for #<Metabolite:0x00007f46b6b84418>

3D-SDF for #<Metabolite:0x00007f46b6b84418>

PDB for #<Metabolite:0x00007f46b6b84418>

3D PDB for #<Metabolite:0x00007f46b6b84418>

SMILES for #<Metabolite:0x00007f46b6b84418>

INCHI for #<Metabolite:0x00007f46b6b84418>

Structure for #<Metabolite:0x00007f46b6b84418>

3D Structure for #<Metabolite:0x00007f46b6b84418>