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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2012-09-12 01:23:27 UTC

Update Date

2023-02-21 17:27:15 UTC

HMDB ID

HMDB0039853

Secondary Accession Numbers

HMDB39853

Metabolite Identification

Common Name

3,5,6-Trichloro-2-pyridinol

Description

3,5,6-Trichloro-2-pyridinol belongs to the class of organic compounds known as polyhalopyridines. These are organic compounds containing a pyridine ring substituted at two or more positions by a halogen atom. 3,5,6-Trichloro-2-pyridinol is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on 3,5,6-Trichloro-2-pyridinol.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
3,5,6-Trichloro-2-pyridin-2-one	ChEBI
2,3,5-trichloro-6-Hydroxypyridine	HMDB
2-Hydroxy-3,5,6-trichloropyridine	HMDB
3,5,6 trichloro 2-Pyridinal	HMDB
3,5,6-trichloro-2(1H)-Pyridinone	HMDB
3,5,6-trichloro-2(1H)-Pyridone	HMDB
3,5,6-trichloro-2-Hydroxypyridine	HMDB
3,5,6-trichloro-2-Pyridinol sodium salt	HMDB, MeSH
3,5,6-trichloro-2-Pyridone	HMDB
3,5,6-Trichloropyridin-2-ol	HMDB
3,5,6-Trichloropyridine-2-ol	HMDB
TCP	HMDB
3,5,6-Trichloro-2-pyridinol	ChEBI

Chemical Formula

C₅H₂Cl₃NO

Average Molecular Weight

198.434

Monoisotopic Molecular Weight

196.920196812

IUPAC Name

3,5,6-trichloropyridin-2-ol

Traditional Name

3,5,6-trichloro-2-pyridinol

CAS Registry Number

6515-38-4

SMILES

OC1=NC(Cl)=C(Cl)C=C1Cl

InChI Identifier

InChI=1S/C5H2Cl3NO/c6-2-1-3(7)5(10)9-4(2)8/h1H,(H,9,10)

InChI Key

WCYYAQFQZQEUEN-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as polyhalopyridines. These are organic compounds containing a pyridine ring substituted at two or more positions by a halogen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Halopyridines

Direct Parent

Polyhalopyridines

Alternative Parents

Substituents

Polyhalopyridine
Dihydropyridine
2-halopyridine
Pyridinone
Aryl chloride
Aryl halide
Hydropyridine
Heteroaromatic compound
Lactam
Azacycle
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organochloride
Organohalogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyridone (CHEBI:83490 )
chloropyridine (CHEBI:83490 )

Ontology

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	208 - 209 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	3.21	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	2.56 g/L	ALOGPS
logP	2.97	ALOGPS
logP	3.08	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	8.92	ChemAxon
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	33.12 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	41.67 m³·mol⁻¹	ChemAxon
Polarizability	15.74 Å³	ChemAxon
Number of Rings	1	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+H]+	132.318	30932474
DeepCCS	[M-H]-	129.429	30932474
DeepCCS	[M-2H]-	166.216	30932474
DeepCCS	[M+Na]+	141.43	30932474
AllCCS	[M+H]+	135.8	32859911
AllCCS	[M+H-H2O]+	131.4	32859911
AllCCS	[M+NH4]+	139.9	32859911
AllCCS	[M+Na]+	141.0	32859911
AllCCS	[M-H]-	126.7	32859911
AllCCS	[M+Na-2H]-	128.3	32859911
AllCCS	[M+HCOO]-	130.2	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.	4.21 minutes	32390414
Predicted by Siyang on May 30, 2022	13.3757 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.41 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	127.6 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1483.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	528.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	200.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	385.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	250.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	511.2 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	529.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	343.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1048.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	369.9 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	1115.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	388.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	374.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	662.1 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	450.1 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	216.0 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3,5,6-Trichloro-2-pyridinol	OC1=NC(Cl)=C(Cl)C=C1Cl	2396.4	Standard polar	33892256
3,5,6-Trichloro-2-pyridinol	OC1=NC(Cl)=C(Cl)C=C1Cl	1423.4	Standard non polar	33892256
3,5,6-Trichloro-2-pyridinol	OC1=NC(Cl)=C(Cl)C=C1Cl	1382.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3,5,6-Trichloro-2-pyridinol,1TMS,isomer #1	C[Si](C)(C)OC1=NC(Cl)=C(Cl)C=C1Cl	1499.0	Semi standard non polar	33892256
3,5,6-Trichloro-2-pyridinol,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=NC(Cl)=C(Cl)C=C1Cl	1739.9	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 - 3,5,6-Trichloro-2-pyridinol GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-0900000000-a8d0dcf1238c002d710f	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,5,6-Trichloro-2-pyridinol GC-MS (1 TMS) - 70eV, Positive	splash10-00di-9780000000-182bcca8f562126cdb9a	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,5,6-Trichloro-2-pyridinol GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,5,6-Trichloro-2-pyridinol 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 - 3,5,6-Trichloro-2-pyridinol LC-ESI-ITFT , negative-QTOF	splash10-0002-0900000000-24319f7e7be94aa378aa	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol LC-ESI-ITFT , negative-QTOF	splash10-0002-0900000000-010b5469eb116a1f5336	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol LC-ESI-ITFT , negative-QTOF	splash10-0002-0900000000-446f93186467bb80f954	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol LC-ESI-ITFT , negative-QTOF	splash10-0002-0900000000-ca4140de2afe8e45a966	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol LC-ESI-ITFT , negative-QTOF	splash10-0002-0900000000-18690d81ddad8e55961e	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol LC-ESI-ITFT , negative-QTOF	splash10-0002-0900000000-1ba7f842ee52ab0b3545	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol LC-ESI-ITFT , negative-QTOF	splash10-0002-0900000000-446f93186467bb80f954	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol LC-ESI-ITFT , negative-QTOF	splash10-0002-0900000000-ca4140de2afe8e45a966	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol LC-ESI-ITFT , negative-QTOF	splash10-0002-0900000000-18690d81ddad8e55961e	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol LC-ESI-ITFT , negative-QTOF	splash10-0002-0900000000-97a4d92376f2feb2a410	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol 45V, Negative-QTOF	splash10-0002-0900000000-ca4140de2afe8e45a966	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol 15V, Negative-QTOF	splash10-0002-0900000000-1ba7f842ee52ab0b3545	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol 60V, Negative-QTOF	splash10-0002-0900000000-18690d81ddad8e55961e	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol 35V, Negative-QTOF	splash10-0002-0900000000-010b5469eb116a1f5336	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol 30V, Negative-QTOF	splash10-0002-0900000000-446f93186467bb80f954	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol 42V, Positive-QTOF	splash10-0002-0900000000-5ab93b4876e264f0ebeb	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol 10V, Positive-QTOF	splash10-0002-0900000000-79182d6d8562e3d1c3e6	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol 20V, Positive-QTOF	splash10-0002-0900000000-737c8618e32269b9dd19	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol 40V, Positive-QTOF	splash10-03dj-9800000000-de8d0e47c3e1c02dda93	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol 10V, Negative-QTOF	splash10-0002-2900000000-a180ba0762186c9ea328	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol 20V, Negative-QTOF	splash10-0002-0900000000-7bbe890cf4245dcb94ac	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol 40V, Negative-QTOF	splash10-0007-9400000000-2b3473f74f8f8ee2fa93	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol 10V, Positive-QTOF	splash10-0002-0900000000-1866005ef66d696d94d7	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol 20V, Positive-QTOF	splash10-0002-0900000000-e18eaae99f7e77a4a1b1	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,5,6-Trichloro-2-pyridinol 40V, Positive-QTOF	splash10-0a4i-3900000000-385b94ff7b932615db10	2021-09-25	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

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Blood
Urine

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	Adult (>18 years old)	Both	Normal	32966057	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	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

FDB019509

KNApSAcK ID

Not Available

Chemspider ID

21541

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

23017

PDB ID

Not Available

ChEBI ID

83490

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

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for 3,5,6-Trichloro-2-pyridinol (HMDB0039853)

MOL for HMDB0039853 (3,5,6-Trichloro-2-pyridinol)

3D MOL for HMDB0039853 (3,5,6-Trichloro-2-pyridinol)

3D SDF for HMDB0039853 (3,5,6-Trichloro-2-pyridinol)

3D-SDF for HMDB0039853 (3,5,6-Trichloro-2-pyridinol)

PDB for HMDB0039853 (3,5,6-Trichloro-2-pyridinol)

3D PDB for HMDB0039853 (3,5,6-Trichloro-2-pyridinol)

SMILES for HMDB0039853 (3,5,6-Trichloro-2-pyridinol)

INCHI for HMDB0039853 (3,5,6-Trichloro-2-pyridinol)

Structure for HMDB0039853 (3,5,6-Trichloro-2-pyridinol)

3D Structure for HMDB0039853 (3,5,6-Trichloro-2-pyridinol)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra