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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 19:14:16 UTC

Update Date

2021-09-26 23:14:43 UTC

HMDB ID

HMDB0258054

Secondary Accession Numbers

None

Metabolite Identification

Common Name

(3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one

Description

(3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one belongs to the class of organic compounds known as lactones. These are cyclic esters of hydroxy carboxylic acids, containing a 1-oxacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. Based on a literature review very few articles have been published on (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). (3r,4r,5s,6r)-3,4,5,6-tetrahydroxyoxepan-2-one is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       3.329   0.375   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.369  -0.829   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.829  -0.829   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.131   0.375   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.211   1.876   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.599   2.545   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.599   4.085   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       2.986   1.876   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -0.993   2.837   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -1.633   0.032   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.161  -2.216   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       3.037  -2.216   0.000  0.00  0.00           O+0
CONECT    1    2    8                                                       
CONECT    2    1    3   12                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    9                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    1                                                       
CONECT    9    5                                                            
CONECT   10    4                                                            
CONECT   11    3                                                            
CONECT   12    2                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₆H₁₀O₆

Average Molecular Weight

178.14

Monoisotopic Molecular Weight

178.047738042

IUPAC Name

3,4,5,6-tetrahydroxyoxepan-2-one

Traditional Name

3,4,5,6-tetrahydroxyoxepan-2-one

CAS Registry Number

Not Available

SMILES

OC1COC(=O)C(O)C(O)C1O

InChI Identifier

InChI=1S/C6H10O6/c7-2-1-12-6(11)5(10)4(9)3(2)8/h2-5,7-10H,1H2

InChI Key

WTXGYGWMPUGBAL-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as lactones. These are cyclic esters of hydroxy carboxylic acids, containing a 1-oxacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactones

Sub Class

Not Available

Direct Parent

Lactones

Alternative Parents

Substituents

Caprolactone
Oxepane
1,2-diol
Carboxylic acid ester
Lactone
Secondary alcohol
Carboxylic acid derivative
Oxacycle
Monocarboxylic acid or derivatives
Polyol
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Alcohol
Organooxygen compound
Organic oxide
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-2.3	ALOGPS
logP	-2.7	ChemAxon
logS	0.51	ALOGPS
pKa (Strongest Acidic)	11.61	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	107.22 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	34.78 m³·mol⁻¹	ChemAxon
Polarizability	15.17 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	137.09	30932474
DeepCCS	[M-H]-	134.098	30932474
DeepCCS	[M-2H]-	170.943	30932474
DeepCCS	[M+Na]+	146.215	30932474
AllCCS	[M+H]+	139.8	32859911
AllCCS	[M+H-H2O]+	135.4	32859911
AllCCS	[M+NH4]+	143.9	32859911
AllCCS	[M+Na]+	145.0	32859911
AllCCS	[M-H]-	129.6	32859911
AllCCS	[M+Na-2H]-	130.5	32859911
AllCCS	[M+HCOO]-	131.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one	OC1COC(=O)C(O)C(O)C1O	4013.0	Standard polar	33892256
(3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one	OC1COC(=O)C(O)C(O)C1O	1784.4	Standard non polar	33892256
(3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one	OC1COC(=O)C(O)C(O)C1O	1726.9	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (Non-derivatized) - 70eV, Positive	splash10-06rl-9400000000-9e4502053b3fe09f123e	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TMS_3_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TMS_3_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TMS_4_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

10637462

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

15300729

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for (3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one (HMDB0258054)

MOL for HMDB0258054 ((3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one)

3D MOL for HMDB0258054 ((3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one)

3D SDF for HMDB0258054 ((3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one)

3D-SDF for HMDB0258054 ((3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one)

PDB for HMDB0258054 ((3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one)

3D PDB for HMDB0258054 ((3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one)

SMILES for HMDB0258054 ((3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one)

INCHI for HMDB0258054 ((3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one)

Structure for HMDB0258054 ((3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one)

3D Structure for HMDB0258054 ((3R,4R,5S,6R)-3,4,5,6-Tetrahydroxyoxepan-2-one)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra