Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2006-08-13 10:46:17 UTC

Update Date

2023-02-21 17:16:54 UTC

HMDB ID

HMDB0004094

Secondary Accession Numbers

HMDB04094

Metabolite Identification

Common Name

Indoxyl

Description

Indoxyl, also known as 1H-indol-3-ol, belongs to the class of organic compounds known as hydroxyindoles. These are organic compounds containing an indole moiety that carries a hydroxyl group. Indoxyl is isomeric with oxindol and is obtained as an oily liquid. Indoxyl exists in all living organisms, ranging from bacteria to humans. Indoxyl is obtained from indican, which is a glycoside. Obermayer's reagent is a dilute solution FeCl3 in hydrochloric acid. The hydrolysis of indican yields β-D-glucose and indoxyl. Indigo dye is a product of the reaction of indoxyl by a mild oxidizing agent such as atmospheric oxygen. In chemistry, indoxyl is a nitrogenous substance with the chemical formula: C8H7NO. Indoxyl can be found in urine and is titrated with Obermayer's reagent.

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-indol-3-Ol	ChEBI

Chemical Formula

C₈H₇NO

Average Molecular Weight

133.1473

Monoisotopic Molecular Weight

133.052763851

IUPAC Name

1H-indol-3-ol

Traditional Name

indoxyl

CAS Registry Number

480-93-3

SMILES

OC1=CNC2=CC=CC=C12

InChI Identifier

InChI=1S/C8H7NO/c10-8-5-9-7-4-2-1-3-6(7)8/h1-5,9-10H

InChI Key

PCKPVGOLPKLUHR-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxyindoles. These are organic compounds containing an indole moiety that carries a hydroxyl group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Hydroxyindoles

Direct Parent

Hydroxyindoles

Alternative Parents

Substituents

Hydroxyindole
Indole
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

hydroxyindoles (CHEBI:17840 )
a small molecule (INDOXYL )

Ontology

Not Available

Endogenous (HMDB: HMDB0004094)

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)

Process

Not Available

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	7.67 g/L	ALOGPS
logP	1.29	ALOGPS
logP	1.77	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	9.15	ChemAxon
pKa (Strongest Basic)	-6.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	36.02 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	39.13 m³·mol⁻¹	ChemAxon
Polarizability	13.78 Å³	ChemAxon
Number of Rings	2	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
DeepCCS	[M-2H]-	157.457	30932474
DeepCCS	[M+Na]+	132.5	30932474
AllCCS	[M+H]+	126.6	32859911
AllCCS	[M+H-H2O]+	121.6	32859911
AllCCS	[M+NH4]+	131.2	32859911
AllCCS	[M+Na]+	132.5	32859911
AllCCS	[M-H]-	123.5	32859911
AllCCS	[M+Na-2H]-	124.6	32859911
AllCCS	[M+HCOO]-	125.8	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. Predicted by Afia on May 17, 2022.	3.15 minutes	32390414
Predicted by Siyang on May 30, 2022	11.9368 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.98 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1864.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	433.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	144.9 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	284.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	318.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	499.1 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	515.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	171.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	931.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	341.1 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	1199.4 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	400.6 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	372.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	557.6 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	269.3 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	156.8 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Indoxyl	OC1=CNC2=CC=CC=C12	2541.5	Standard polar	33892256
Indoxyl	OC1=CNC2=CC=CC=C12	1528.1	Standard non polar	33892256
Indoxyl	OC1=CNC2=CC=CC=C12	1508.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Indoxyl,1TMS,isomer #1	C[Si](C)(C)OC1=C[NH]C2=CC=CC=C12	1602.3	Semi standard non polar	33892256
Indoxyl,1TMS,isomer #2	C[Si](C)(C)N1C=C(O)C2=CC=CC=C21	1706.1	Semi standard non polar	33892256
Indoxyl,2TMS,isomer #1	C[Si](C)(C)OC1=CN([Si](C)(C)C)C2=CC=CC=C12	1782.5	Semi standard non polar	33892256
Indoxyl,2TMS,isomer #1	C[Si](C)(C)OC1=CN([Si](C)(C)C)C2=CC=CC=C12	1708.8	Standard non polar	33892256
Indoxyl,2TMS,isomer #1	C[Si](C)(C)OC1=CN([Si](C)(C)C)C2=CC=CC=C12	1710.5	Standard polar	33892256
Indoxyl,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=C[NH]C2=CC=CC=C12	1869.4	Semi standard non polar	33892256
Indoxyl,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C=C(O)C2=CC=CC=C21	1958.2	Semi standard non polar	33892256
Indoxyl,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C2=CC=CC=C12	2156.8	Semi standard non polar	33892256
Indoxyl,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C2=CC=CC=C12	2120.6	Standard non polar	33892256
Indoxyl,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=CN([Si](C)(C)C(C)(C)C)C2=CC=CC=C12	2011.6	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - Indoxyl GC-MS (2 TMS)	splash10-004i-3980000000-520b4525adaeb185fb13	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Indoxyl GC-MS (Non-derivatized)	splash10-004i-3980000000-520b4525adaeb185fb13	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Indoxyl GC-MS (Non-derivatized) - 70eV, Positive	splash10-0kai-1900000000-1c5e163741d871a2c138	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Indoxyl GC-MS (1 TMS) - 70eV, Positive	splash10-0fl3-6910000000-0c8f4cb37b60dcecf8ea	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Indoxyl 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
Experimental LC-MS/MS	LC-MS/MS Spectrum - Indoxyl Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-001i-0900000000-e2d4dbd9b806b29ce214	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Indoxyl Quattro_QQQ 25V, Positive-QTOF (Annotated)	splash10-056r-9500000000-263e6cbbc9fbea4d1fe2	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Indoxyl Quattro_QQQ 40V, Positive-QTOF (Annotated)	splash10-004i-9000000000-601cd8ae4909db7a541a	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Indoxyl 10V, Negative-QTOF	splash10-001i-1900000000-0276e7599b0c044e16ca	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Indoxyl 20V, Negative-QTOF	splash10-003r-8900000000-1a948ecd165e51423035	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Indoxyl 20V, Positive-QTOF	splash10-0a4i-6900000000-e7a7e7fb048f732eb685	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Indoxyl 10V, Positive-QTOF	splash10-001i-4900000000-e34a5c59b0cce2170e4f	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Indoxyl 40V, Positive-QTOF	splash10-004i-9000000000-271db1608159a875a61c	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Indoxyl 40V, Negative-QTOF	splash10-0006-9100000000-e357308e88e379d8eb0b	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indoxyl 10V, Positive-QTOF	splash10-001i-0900000000-ce70e056e1f4cfdf3761	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indoxyl 20V, Positive-QTOF	splash10-001i-0900000000-9beba85555a54c1f672e	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indoxyl 40V, Positive-QTOF	splash10-0kui-7900000000-c36b8119a51196a1f474	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indoxyl 10V, Negative-QTOF	splash10-001i-0900000000-0d126f50596b5c4ae9ec	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indoxyl 20V, Negative-QTOF	splash10-001i-0900000000-d5b63c4616a3ca6983c2	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indoxyl 40V, Negative-QTOF	splash10-0udi-2900000000-f4d199baa93fba2d315c	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indoxyl 10V, Positive-QTOF	splash10-001i-0900000000-ac524f6f858437766e2f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indoxyl 20V, Positive-QTOF	splash10-001i-1900000000-1064492c92995ca99566	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indoxyl 40V, Positive-QTOF	splash10-004i-9300000000-62b87115059cfc657adc	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indoxyl 10V, Negative-QTOF	splash10-001i-0900000000-a956a3a0009c6965897a	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indoxyl 20V, Negative-QTOF	splash10-001i-0900000000-7b07769eadb95204ac58	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indoxyl 40V, Negative-QTOF	splash10-001i-0900000000-fea25d8ed304aa380484	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Experimental 1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	2021-10-10	Wishart Lab	View Spectrum
Experimental 1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	2021-10-10	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	2012-12-05	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

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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Indoxyl

METLIN ID

7014

PubChem Compound

50591

PDB ID

Not Available

ChEBI ID

17840

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Stoppani, Andres O. M. Formation of indoxyl from nitro and amino derivatives of benzene. Revista de la Sociedad Argentina de Biologia (1943), 19 421-34.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Achtergael W, Michielsen D, Gorus FK, Gerlo E: Indoxyl sulphate and the purple urine bag syndrome: a case report. Acta Clin Belg. 2006 Jan-Feb;61(1):38-41. [PubMed:16673616 ]
Delisle GJ, Ley A: Rapid detection of Escherichia coli in urine samples by a new chromogenic beta-glucuronidase assay. J Clin Microbiol. 1989 Apr;27(4):778-9. [PubMed:2656750 ]

Showing metabocard for Indoxyl (HMDB0004094)

MOL for HMDB0004094 (Indoxyl)

3D MOL for HMDB0004094 (Indoxyl)

3D SDF for HMDB0004094 (Indoxyl)

3D-SDF for HMDB0004094 (Indoxyl)

PDB for HMDB0004094 (Indoxyl)

3D PDB for HMDB0004094 (Indoxyl)

SMILES for HMDB0004094 (Indoxyl)

INCHI for HMDB0004094 (Indoxyl)

Structure for HMDB0004094 (Indoxyl)

3D Structure for HMDB0004094 (Indoxyl)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra