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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (20) Show 20 proteins XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-05-17 00:50:38 UTC

Update Date

2022-03-07 03:17:42 UTC

HMDB ID

HMDB0060301

Secondary Accession Numbers

HMDB60301

Metabolite Identification

Common Name

(1S,2R)-Naphthalene 1,2-oxide

Description

(1S,2R)-Naphthalene 1,2-oxide belongs to the class of organic compounds known as naphthalenes. Naphthalenes are compounds containing a naphthalene moiety, which consists of two fused benzene rings (1S,2R)-Naphthalene 1,2-oxide is an extremely weak basic (essentially neutral) compound (based on its pKa) (1S,2R)-Naphthalene 1,2-oxide exists in all living organisms, ranging from bacteria to humans. These are organic compounds containing a benzene ring fused to an oxepine ring.

Structure

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

HEADER    PROTEIN                                 13-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-AUG-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    6    7                                                       
CONECT    6    5    9                                                       
CONECT    7    3    5    8                                                  
CONECT    8    4    7   10                                                  
CONECT    9    6   10   11   12                                             
CONECT   10    8    9   11   13                                             
CONECT   11    9   10                                                       
CONECT   12    9                                                            
CONECT   13   10                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   30    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(1S,2R)-Naphthalene epoxide	Kegg

Chemical Formula

C₁₀H₈O

Average Molecular Weight

144.1699

Monoisotopic Molecular Weight

144.057514878

IUPAC Name

(1aS,7aR)-1aH,7aH-naphtho[1,2-b]oxirene

Traditional Name

(1aS,7aR)-1aH,7aH-naphtho[1,2-b]oxirene

CAS Registry Number

Not Available

SMILES

[H][C@]12O[C@@]1([H])C1=CC=CC=C1C=C2

InChI Identifier

InChI=1S/C10H8O/c1-2-4-8-7(3-1)5-6-9-10(8)11-9/h1-6,9-10H/t9-,10+/m1/s1

InChI Key

XQIJIALOJPIKGX-ZJUUUORDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as naphthalenes. Naphthalenes are compounds containing a naphthalene moiety, which consists of two fused benzene rings.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Naphthalenes

Sub Class

Not Available

Direct Parent

Naphthalenes

Alternative Parents

Substituents

Naphthalene
Oxacycle
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

naphthalenes (CHEBI:34001 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0060301)

Source

Exogenous

Exogenous (HMDB: HMDB0060301)

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
Water Solubility	0.28 g/L	ALOGPS
logP	1.89	ALOGPS
logP	2.16	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	12.53 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	43.87 m³·mol⁻¹	ChemAxon
Polarizability	15.26 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	131.659	31661259
DarkChem	[M-H]-	128.796	31661259
DeepCCS	[M-2H]-	166.854	30932474
DeepCCS	[M+Na]+	141.285	30932474
AllCCS	[M+H]+	130.6	32859911
AllCCS	[M+H-H2O]+	125.8	32859911
AllCCS	[M+NH4]+	135.0	32859911
AllCCS	[M+Na]+	136.3	32859911
AllCCS	[M-H]-	129.6	32859911
AllCCS	[M+Na-2H]-	130.0	32859911
AllCCS	[M+HCOO]-	130.6	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm √ó 2.1 mm; 1.7 Œºmparticle diameter). Predicted by Afia on May 17, 2022.	5.65 minutes	32390414
Predicted by Siyang on May 30, 2022	14.5711 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.84 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2191.2 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	532.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	213.6 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	363.7 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	315.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	557.2 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	657.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	117.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1264.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	448.2 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1230.2 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	460.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	421.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	554.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	455.8 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	80.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(1S,2R)-Naphthalene 1,2-oxide	[H][C@]12O[C@@]1([H])C1=CC=CC=C1C=C2	2253.6	Standard polar	33892256
(1S,2R)-Naphthalene 1,2-oxide	[H][C@]12O[C@@]1([H])C1=CC=CC=C1C=C2	1258.0	Standard non polar	33892256
(1S,2R)-Naphthalene 1,2-oxide	[H][C@]12O[C@@]1([H])C1=CC=CC=C1C=C2	1313.5	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 - (1S,2R)-Naphthalene 1,2-oxide GC-MS (Non-derivatized) - 70eV, Positive	splash10-0v03-2900000000-47ac39354a6928036f2d	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (1S,2R)-Naphthalene 1,2-oxide GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (1S,2R)-Naphthalene 1,2-oxide GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (1S,2R)-Naphthalene 1,2-oxide 10V, Positive-QTOF	splash10-0002-0900000000-8e17fcee1e69025d7b19	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (1S,2R)-Naphthalene 1,2-oxide 20V, Positive-QTOF	splash10-0002-0900000000-5b1ddedd928252655953	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (1S,2R)-Naphthalene 1,2-oxide 40V, Positive-QTOF	splash10-0ufr-9700000000-1e74dedc14082f2542df	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (1S,2R)-Naphthalene 1,2-oxide 10V, Negative-QTOF	splash10-0006-0900000000-82c24c2437621729b2df	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (1S,2R)-Naphthalene 1,2-oxide 20V, Negative-QTOF	splash10-0006-0900000000-1f87d4685bd2dc480922	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (1S,2R)-Naphthalene 1,2-oxide 40V, Negative-QTOF	splash10-0uxu-1900000000-1566ad7e8623ac3f4b54	2017-10-06	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane (predicted from logP)

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

9269891

KEGG Compound ID

C14787

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11094749

PDB ID

Not Available

ChEBI ID

34001

Food Biomarker Ontology

Not Available

VMH ID

M00034

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]

Only showing the first 10 proteins. There are 20 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details

1. Glutathione S-transferase Mu 2

General function:: Involved in glutathione transferase activity
Specific function:: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles.
Gene Name:: GSTM2
Uniprot ID:: P28161
Molecular weight:: 25744.395

Reactions

(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1R)-Glutathionyl-(2R)-hydroxy-1,2-dihydronaphthalene	details
(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1S)-Hydroxy-(2S)-glutathionyl-1,2-dihydronaphthalene	details

Enzyme Details

2. Glutathione S-transferase Mu 1

General function:: Involved in glutathione transferase activity
Specific function:: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles.
Gene Name:: GSTM1
Uniprot ID:: P09488
Molecular weight:: 25711.555

Reactions

(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1R)-Glutathionyl-(2R)-hydroxy-1,2-dihydronaphthalene	details
(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1S)-Hydroxy-(2S)-glutathionyl-1,2-dihydronaphthalene	details

Enzyme Details

3. Glutathione S-transferase kappa 1

General function:: Involved in protein disulfide oxidoreductase activity
Specific function:: Significant glutathione conjugating activity is found only with the model substrate, 1-chloro-2,4-dinitrobenzene (CDNB).
Gene Name:: GSTK1
Uniprot ID:: Q9Y2Q3
Molecular weight:: 31565.605

Reactions

(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1R)-Glutathionyl-(2R)-hydroxy-1,2-dihydronaphthalene	details
(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1S)-Hydroxy-(2S)-glutathionyl-1,2-dihydronaphthalene	details

Enzyme Details

4. Microsomal glutathione S-transferase 3

General function:: Involved in glutathione transferase activity
Specific function:: Also functions as a glutathione peroxidase.
Gene Name:: MGST3
Uniprot ID:: O14880
Molecular weight:: 16516.185

Reactions

(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1R)-Glutathionyl-(2R)-hydroxy-1,2-dihydronaphthalene	details
(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1S)-Hydroxy-(2S)-glutathionyl-1,2-dihydronaphthalene	details

Enzyme Details

5. Glutathione S-transferase Mu 3

General function:: Involved in glutathione transferase activity
Specific function:: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. May govern uptake and detoxification of both endogenous compounds and xenobiotics at the testis and brain blood barriers.
Gene Name:: GSTM3
Uniprot ID:: P21266
Molecular weight:: 26559.32

Reactions

(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1R)-Glutathionyl-(2R)-hydroxy-1,2-dihydronaphthalene	details
(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1S)-Hydroxy-(2S)-glutathionyl-1,2-dihydronaphthalene	details

Enzyme Details

6. Glutathione S-transferase A1

General function:: Involved in glutathione transferase activity
Specific function:: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles.
Gene Name:: GSTA1
Uniprot ID:: P08263
Molecular weight:: 25630.785

Reactions

(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1R)-Glutathionyl-(2R)-hydroxy-1,2-dihydronaphthalene	details
(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1S)-Hydroxy-(2S)-glutathionyl-1,2-dihydronaphthalene	details

Enzyme Details

7. Microsomal glutathione S-transferase 1

General function:: Involved in glutathione transferase activity
Specific function:: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. Has a wide substrate specificity.
Gene Name:: MGST1
Uniprot ID:: P10620
Molecular weight:: 17598.45

Reactions

(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1R)-Glutathionyl-(2R)-hydroxy-1,2-dihydronaphthalene	details
(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1S)-Hydroxy-(2S)-glutathionyl-1,2-dihydronaphthalene	details

Enzyme Details

8. Glutathione S-transferase Mu 4

General function:: Involved in glutathione transferase activity
Specific function:: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. Active on 1-chloro-2,4-dinitrobenzene.
Gene Name:: GSTM4
Uniprot ID:: Q03013
Molecular weight:: 25561.095

Reactions

(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1R)-Glutathionyl-(2R)-hydroxy-1,2-dihydronaphthalene	details
(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1S)-Hydroxy-(2S)-glutathionyl-1,2-dihydronaphthalene	details

Enzyme Details

9. Glutathione S-transferase Mu 5

General function:: Involved in glutathione transferase activity
Specific function:: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles.
Gene Name:: GSTM5
Uniprot ID:: P46439
Molecular weight:: 25674.455

Reactions

(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1R)-Glutathionyl-(2R)-hydroxy-1,2-dihydronaphthalene	details
(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1S)-Hydroxy-(2S)-glutathionyl-1,2-dihydronaphthalene	details

Enzyme Details

10. Microsomal glutathione S-transferase 2

General function:: Involved in enzyme activator activity
Specific function:: Can catalyze the production of LTC4 from LTA4 and reduced glutathione. Can catalyze the conjugation of 1-chloro-2,4-dinitrobenzene with reduced glutathione.
Gene Name:: MGST2
Uniprot ID:: Q99735
Molecular weight:: 16620.4

Reactions

(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1R)-Glutathionyl-(2R)-hydroxy-1,2-dihydronaphthalene	details
(1S,2R)-Naphthalene 1,2-oxide + Glutathione → (1S)-Hydroxy-(2S)-glutathionyl-1,2-dihydronaphthalene	details

Only showing the first 10 proteins. There are 20 proteins in total.

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Showing metabocard for (1S,2R)-Naphthalene 1,2-oxide (HMDB0060301)

MOL for HMDB0060301 ((1S,2R)-Naphthalene 1,2-oxide)

3D MOL for HMDB0060301 ((1S,2R)-Naphthalene 1,2-oxide)

3D SDF for HMDB0060301 ((1S,2R)-Naphthalene 1,2-oxide)

3D-SDF for HMDB0060301 ((1S,2R)-Naphthalene 1,2-oxide)

PDB for HMDB0060301 ((1S,2R)-Naphthalene 1,2-oxide)

3D PDB for HMDB0060301 ((1S,2R)-Naphthalene 1,2-oxide)

SMILES for HMDB0060301 ((1S,2R)-Naphthalene 1,2-oxide)

INCHI for HMDB0060301 ((1S,2R)-Naphthalene 1,2-oxide)

Structure for HMDB0060301 ((1S,2R)-Naphthalene 1,2-oxide)

3D Structure for HMDB0060301 ((1S,2R)-Naphthalene 1,2-oxide)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

Enzymes

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions

Reactions