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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 23:47:08 UTC

Update Date

2021-09-26 22:56:03 UTC

HMDB ID

HMDB0246772

Secondary Accession Numbers

None

Metabolite Identification

Common Name

5-Chlorouracil

Description

5-Chlorouracil belongs to the class of organic compounds known as halopyrimidines. These are aromatic compounds containing a halogen atom linked to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Based on a literature review a significant number of articles have been published on 5-Chlorouracil. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-chlorouracil is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-Chlorouracil 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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₄H₃ClN₂O₂

Average Molecular Weight

146.53

Monoisotopic Molecular Weight

145.988305

IUPAC Name

5-chloro-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

5-chlorouracil

CAS Registry Number

Not Available

SMILES

ClC1=CNC(=O)NC1=O

InChI Identifier

InChI=1S/C4H3ClN2O2/c5-2-1-6-4(9)7-3(2)8/h1H,(H2,6,7,8,9)

InChI Key

ZFTBZKVVGZNMJR-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as halopyrimidines. These are aromatic compounds containing a halogen atom linked to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Halopyrimidines

Alternative Parents

Substituents

Halopyrimidine
Pyrimidone
Aryl chloride
Aryl halide
Hydropyrimidine
Heteroaromatic compound
Vinylogous amide
Lactam
Urea
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

organochlorine compound (CHEBI:60762 )

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	-0.33	ALOGPS
logP	-0.19	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	7.47	ChemAxon
pKa (Strongest Basic)	-6.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	58.2 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	30.76 m³·mol⁻¹	ChemAxon
Polarizability	11.52 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]+	123.752	30932474
DeepCCS	[M-H]-	120.547	30932474
DeepCCS	[M-2H]-	157.005	30932474
DeepCCS	[M+Na]+	132.309	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	8.8804 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.8 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	557.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	344.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	89.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	243.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	59.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	272.0 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	282.0 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	332.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	594.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	102.9 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	701.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	231.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	263.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	646.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	303.1 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	292.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Chlorouracil	ClC1=CNC(=O)NC1=O	2303.4	Standard polar	33892256
5-Chlorouracil	ClC1=CNC(=O)NC1=O	1475.0	Standard non polar	33892256
5-Chlorouracil	ClC1=CNC(=O)NC1=O	1724.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Chlorouracil,1TMS,isomer #1	C[Si](C)(C)N1C=C(Cl)C(=O)[NH]C1=O	1570.6	Semi standard non polar	33892256
5-Chlorouracil,1TMS,isomer #1	C[Si](C)(C)N1C=C(Cl)C(=O)[NH]C1=O	1606.7	Standard non polar	33892256
5-Chlorouracil,1TMS,isomer #1	C[Si](C)(C)N1C=C(Cl)C(=O)[NH]C1=O	2030.2	Standard polar	33892256
5-Chlorouracil,1TMS,isomer #2	C[Si](C)(C)N1C(=O)[NH]C=C(Cl)C1=O	1519.3	Semi standard non polar	33892256
5-Chlorouracil,1TMS,isomer #2	C[Si](C)(C)N1C(=O)[NH]C=C(Cl)C1=O	1540.7	Standard non polar	33892256
5-Chlorouracil,1TMS,isomer #2	C[Si](C)(C)N1C(=O)[NH]C=C(Cl)C1=O	2029.7	Standard polar	33892256
5-Chlorouracil,2TMS,isomer #1	C[Si](C)(C)N1C=C(Cl)C(=O)N([Si](C)(C)C)C1=O	1708.3	Semi standard non polar	33892256
5-Chlorouracil,2TMS,isomer #1	C[Si](C)(C)N1C=C(Cl)C(=O)N([Si](C)(C)C)C1=O	1724.8	Standard non polar	33892256
5-Chlorouracil,2TMS,isomer #1	C[Si](C)(C)N1C=C(Cl)C(=O)N([Si](C)(C)C)C1=O	1822.6	Standard polar	33892256
5-Chlorouracil,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C=C(Cl)C(=O)[NH]C1=O	1838.3	Semi standard non polar	33892256
5-Chlorouracil,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C=C(Cl)C(=O)[NH]C1=O	1801.7	Standard non polar	33892256
5-Chlorouracil,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C=C(Cl)C(=O)[NH]C1=O	2122.6	Standard polar	33892256
5-Chlorouracil,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C(=O)[NH]C=C(Cl)C1=O	1745.9	Semi standard non polar	33892256
5-Chlorouracil,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C(=O)[NH]C=C(Cl)C1=O	1767.0	Standard non polar	33892256
5-Chlorouracil,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C(=O)[NH]C=C(Cl)C1=O	2096.3	Standard polar	33892256
5-Chlorouracil,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C=C(Cl)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2105.5	Semi standard non polar	33892256
5-Chlorouracil,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C=C(Cl)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2136.4	Standard non polar	33892256
5-Chlorouracil,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C=C(Cl)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2029.9	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chlorouracil GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-5900000000-cb5edf19602997d6b054	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chlorouracil 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 - 5-Chlorouracil 10V, Positive-QTOF	splash10-0002-0900000000-95eab36c910aa0729a1f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chlorouracil 20V, Positive-QTOF	splash10-0002-2900000000-e94308f2eb530f3f8481	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chlorouracil 40V, Positive-QTOF	splash10-0006-9000000000-d56b6d125e02fac5c3e9	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chlorouracil 10V, Negative-QTOF	splash10-0006-0900000000-0589d147857279e4eb6d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chlorouracil 20V, Negative-QTOF	splash10-0006-9000000000-377b0e010d72a4a9032f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chlorouracil 40V, Negative-QTOF	splash10-0006-9000000000-90726b17dc36e29c5299	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	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

14985

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

60762

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 5-Chlorouracil (HMDB0246772)

MOL for HMDB0246772 (5-Chlorouracil)

3D MOL for HMDB0246772 (5-Chlorouracil)

3D SDF for HMDB0246772 (5-Chlorouracil)

3D-SDF for HMDB0246772 (5-Chlorouracil)

PDB for HMDB0246772 (5-Chlorouracil)

3D PDB for HMDB0246772 (5-Chlorouracil)

SMILES for HMDB0246772 (5-Chlorouracil)

INCHI for HMDB0246772 (5-Chlorouracil)

Structure for HMDB0246772 (5-Chlorouracil)

3D Structure for HMDB0246772 (5-Chlorouracil)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra