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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (1) Show 1 protein XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2008-08-08 10:45:44 UTC

Update Date

2023-02-21 17:17:20 UTC

HMDB ID

HMDB0006779

Secondary Accession Numbers

HMDB06779

Metabolite Identification

Common Name

Indole-5,6-quinone

Description

Indole-5,6-quinone belongs to the class of organic compounds known as indoles and derivatives. These are organic compounds containing an indole, which is a bicyclic ring system made up of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring. Indole-5,6-quinone exists in all living organisms, ranging from bacteria to humans. In humans, indole-5,6-quinone is involved in the metabolic disorder called hawkinsinuria. Indole-5,6-quinone has been detected, but not quantified in, several different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), domestic pigs (Sus scrofa domestica), and milk (cow). This could make indole-5,6-quinone a potential biomarker for the consumption of these foods. Indole-5,6-quinone is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Indole-5,6-quinone.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
1H-Indole-5,6-dione	HMDB
Indole-5,6 quinone	HMDB

Chemical Formula

C₈H₅NO₂

Average Molecular Weight

147.1308

Monoisotopic Molecular Weight

147.032028409

IUPAC Name

5,6-dihydro-1H-indole-5,6-dione

Traditional Name

indole-5,6-quinone

CAS Registry Number

582-59-2

SMILES

O=C1C=C2NC=CC2=CC1=O

InChI Identifier

InChI=1S/C8H5NO2/c10-7-3-5-1-2-9-6(5)4-8(7)11/h1-4,9H

InChI Key

IGGVVGHJSQSLFO-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indoles and derivatives. These are organic compounds containing an indole, which is a bicyclic ring system made up of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Not Available

Direct Parent

Indoles and derivatives

Alternative Parents

Substituents

Indole or derivatives
Pyrrole
Vinylogous amide
Heteroaromatic compound
Ketone
Cyclic ketone
Azacycle
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

quinone (CHEBI:27406 )
indoledione (CHEBI:27406 )
an alkaloid (CPD-12373 )

Ontology

Not Available

Endogenous (HMDB: HMDB0006779)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Milk and milk product

Unfermented milk

Milk (Cow) (FooDB: FOOD00618)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Tyrosine Metabolism (PathBank: SMP0087328)
Tyrosine Metabolism (HMDB: HMDB0006779)
Eumelanin Biosynthesis (PathBank: SMP0121124)

Disease pathway

Tyrosinemia, Transient, of the Newborn (PathBank: SMP0120779)
Hawkinsinuria (PathBank: SMP0120711)
Tyrosinemia Type I (PathBank: SMP0120729)
Alkaptonuria (PathBank: SMP0120453)
Dopamine beta-Hydroxylase Deficiency (PathBank: SMP0120563)
Monoamine Oxidase-A Deficiency (MAO-A) (PathBank: SMP0120817)

Drug action pathway

Disulfiram Action Pathway (HMDB: HMDB0006779)
Disulfiram Action Pathway (PathBank: SMP0000429)

Role

Not Available

Physical Properties

State

Solid

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	10.5 g/L	ALOGPS
logP	0.09	ALOGPS
logP	0.65	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Basic)	4.01	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	46.17 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	42.15 m³·mol⁻¹	ChemAxon
Polarizability	13.76 Å³	ChemAxon
Number of Rings	2	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
DarkChem	[M+H]+	131.235	31661259
DarkChem	[M-H]-	128.328	31661259
DeepCCS	[M+H]+	125.278	30932474
DeepCCS	[M-H]-	121.498	30932474
DeepCCS	[M-2H]-	158.848	30932474
DeepCCS	[M+Na]+	134.182	30932474
AllCCS	[M+H]+	128.9	32859911
AllCCS	[M+H-H2O]+	124.1	32859911
AllCCS	[M+NH4]+	133.3	32859911
AllCCS	[M+Na]+	134.6	32859911
AllCCS	[M-H]-	126.6	32859911
AllCCS	[M+Na-2H]-	127.4	32859911
AllCCS	[M+HCOO]-	128.3	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 × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022.	3.16 minutes	32390414
Predicted by Siyang on May 30, 2022	11.0903 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.66 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1284.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	364.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	97.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	235.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	78.2 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	350.8 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	455.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	214.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	786.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	144.3 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	1134.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	258.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	286.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	694.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	220.6 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	233.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Indole-5,6-quinone	O=C1C=C2NC=CC2=CC1=O	2667.4	Standard polar	33892256
Indole-5,6-quinone	O=C1C=C2NC=CC2=CC1=O	1915.4	Standard non polar	33892256
Indole-5,6-quinone	O=C1C=C2NC=CC2=CC1=O	1887.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Indole-5,6-quinone,1TMS,isomer #1	C[Si](C)(C)N1C=CC2=CC(=O)C(=O)C=C21	1971.1	Semi standard non polar	33892256
Indole-5,6-quinone,1TMS,isomer #1	C[Si](C)(C)N1C=CC2=CC(=O)C(=O)C=C21	1836.0	Standard non polar	33892256
Indole-5,6-quinone,1TMS,isomer #1	C[Si](C)(C)N1C=CC2=CC(=O)C(=O)C=C21	2604.2	Standard polar	33892256
Indole-5,6-quinone,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C=CC2=CC(=O)C(=O)C=C21	2189.3	Semi standard non polar	33892256
Indole-5,6-quinone,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C=CC2=CC(=O)C(=O)C=C21	2041.2	Standard non polar	33892256
Indole-5,6-quinone,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C=CC2=CC(=O)C(=O)C=C21	2764.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Indole-5,6-quinone GC-MS (Non-derivatized) - 70eV, Positive	splash10-066v-6900000000-1dca4f608ca530016412	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Indole-5,6-quinone 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 - Indole-5,6-quinone 10V, Positive-QTOF	splash10-0002-0900000000-0cf3a823a731cd4e7a64	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indole-5,6-quinone 20V, Positive-QTOF	splash10-00dj-0900000000-81eabafffbd73c3732d0	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indole-5,6-quinone 40V, Positive-QTOF	splash10-004i-9400000000-a1268508f67a658cecf5	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indole-5,6-quinone 10V, Negative-QTOF	splash10-0002-0900000000-efe9cb1e2b58b04208a1	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indole-5,6-quinone 20V, Negative-QTOF	splash10-0002-0900000000-37f54dda461b2c0102c3	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indole-5,6-quinone 40V, Negative-QTOF	splash10-014j-0900000000-775f13193ba5fc2154eb	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indole-5,6-quinone 10V, Positive-QTOF	splash10-0002-0900000000-9731758a758f9f924b40	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indole-5,6-quinone 20V, Positive-QTOF	splash10-006t-1900000000-8e368a3b1e151aabfbfa	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indole-5,6-quinone 40V, Positive-QTOF	splash10-0fxx-9700000000-616921cda808497b0d2c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indole-5,6-quinone 10V, Negative-QTOF	splash10-0002-0900000000-7c00c3e5508255ca8248	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indole-5,6-quinone 20V, Negative-QTOF	splash10-0002-0900000000-a13b820d1ef5510928d7	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indole-5,6-quinone 40V, Negative-QTOF	splash10-00kb-0900000000-e18791078884a5a972e8	2021-09-23	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Name	SMPDB/PathBank	KEGG
Tyrosine metabolism	Not Available
Alkaptonuria		Not Available
Hawkinsinuria		Not Available
Tyrosinemia Type I		Not Available
Tyrosinemia, transient, of the newborn		Not Available

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

FDB024077

KNApSAcK ID

Not Available

Chemspider ID

389600

KEGG Compound ID

C05579

BioCyc ID

CPD-12373

BiGG ID

Not Available

Wikipedia Link

Indole-5,6-quinone

METLIN ID

Not Available

PubChem Compound

440728

PDB ID

Not Available

ChEBI ID

27406

Food Biomarker Ontology

Not Available

VMH ID

M03163

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. Tyrosinase

General function:: Involved in oxidoreductase activity
Specific function:: This is a copper-containing oxidase that functions in the formation of pigments such as melanins and other polyphenolic compounds. Catalyzes the rate-limiting conversions of tyrosine to DOPA, DOPA to DOPA-quinone and possibly 5,6-dihydroxyindole to indole-5,6 quinone.
Gene Name:: TYR
Uniprot ID:: P14679
Molecular weight:: 60392.69

Reactions

5,6-Dihydroxyindole + Oxygen → Indole-5,6-quinone + Water	details

Showing metabocard for Indole-5,6-quinone (HMDB0006779)

MOL for HMDB0006779 (Indole-5,6-quinone)

3D MOL for HMDB0006779 (Indole-5,6-quinone)

3D SDF for HMDB0006779 (Indole-5,6-quinone)

3D-SDF for HMDB0006779 (Indole-5,6-quinone)

PDB for HMDB0006779 (Indole-5,6-quinone)

3D PDB for HMDB0006779 (Indole-5,6-quinone)

SMILES for HMDB0006779 (Indole-5,6-quinone)

INCHI for HMDB0006779 (Indole-5,6-quinone)

Structure for HMDB0006779 (Indole-5,6-quinone)

3D Structure for HMDB0006779 (Indole-5,6-quinone)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra

Enzymes

Reactions