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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-05-17 00:59:58 UTC

Update Date

2023-02-21 17:29:58 UTC

HMDB ID

HMDB0060402

Secondary Accession Numbers

HMDB60402

Metabolite Identification

Common Name

5,6-Dihydro-5-fluorouracil

Description

5,6-Dihydro-5-fluorouracil is a metabolite of fluorouracil. Fluorouracil (5-FU or f5U) (sold under the brand names Adrucil, Carac, Efudix, Efudex and Fluoroplex) is a drug that is a pyrimidine analog which is used in the treatment of cancer. It is a suicide inhibitor and works through irreversible inhibition of thymidylate synthase. It belongs to the family of drugs called antimetabolites. It is typically administered with leucovorin. (Wikipedia)

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
5-Fluorodihydrouracil	Kegg
(R)-5-Fluoro-5,6-dihydrouracil	HMDB
DHFU	HMDB
5,6-Dihydrofluorouracil	HMDB
5-Dihydrofluorouracil	HMDB
5-Fluorodihydrouracil, sodium salt	HMDB

Chemical Formula

C₄H₅FN₂O₂

Average Molecular Weight

132.0931

Monoisotopic Molecular Weight

132.033505619

IUPAC Name

5-fluoro-1,3-diazinane-2,4-dione

Traditional Name

5,6-dihydro-5-fluorouracil

CAS Registry Number

Not Available

SMILES

FC1CNC(=O)NC1=O

InChI Identifier

InChI=1S/C4H5FN2O2/c5-2-1-6-4(9)7-3(2)8/h2H,1H2,(H2,6,7,8,9)

InChI Key

RAIRJKWTBBDDAR-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydropyrimidines. Hydropyrimidines are compounds containing a hydrogenated pyrimidine ring (i.E. Containing less than the maximum number of double bonds.).

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Hydropyrimidines

Alternative Parents

Substituents

Hydropyrimidine
5,6-dihydropyrimidine
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Azacycle
Alkyl fluoride
Hydrocarbon derivative
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organofluoride
Organohalogen compound
Organic oxygen compound
Organic nitrogen compound
Alkyl halide
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

9,11,15-octadecatrienoic acid (CHEBI:80624 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0060402)

Organ

Liver (HMDB: HMDB0060402)
Kidney (HMDB: HMDB0060402)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0060402)

Cellular substructure

Cytoplasm (HMDB: HMDB0060402)

Source

Endogenous

Endogenous (HMDB: HMDB0060402)

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	1.99 g/L	ALOGPS
logP	-1.2	ALOGPS
logP	-1	ChemAxon
logS	-0.43	ALOGPS
pKa (Strongest Acidic)	10.66	ChemAxon
pKa (Strongest Basic)	-8.4	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	25.39 m³·mol⁻¹	ChemAxon
Polarizability	10.22 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]+	126.823	30932474
DeepCCS	[M-H]-	123.689	30932474
DeepCCS	[M-2H]-	160.691	30932474
DeepCCS	[M+Na]+	135.553	30932474
AllCCS	[M+H]+	128.9	32859911
AllCCS	[M+H-H2O]+	124.2	32859911
AllCCS	[M+NH4]+	133.3	32859911
AllCCS	[M+Na]+	134.6	32859911
AllCCS	[M-H]-	122.0	32859911
AllCCS	[M+Na-2H]-	124.1	32859911
AllCCS	[M+HCOO]-	126.4	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.	0.69 minutes	32390414
Predicted by Siyang on May 30, 2022	8.7024 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.55 minutes	32390414

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5,6-Dihydro-5-fluorouracil	OC1=NCC(F)C(O)=N1	2184.7	Standard polar	33892256
5,6-Dihydro-5-fluorouracil	OC1=NCC(F)C(O)=N1	1264.8	Standard non polar	33892256
5,6-Dihydro-5-fluorouracil	OC1=NCC(F)C(O)=N1	1322.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5,6-Dihydro-5-fluorouracil,1TMS,isomer #1	C[Si](C)(C)OC1=NCC(F)C(O)=N1	1407.5	Semi standard non polar	33892256
5,6-Dihydro-5-fluorouracil,1TMS,isomer #2	C[Si](C)(C)OC1=NC(O)=NCC1F	1386.2	Semi standard non polar	33892256
5,6-Dihydro-5-fluorouracil,2TMS,isomer #1	C[Si](C)(C)OC1=NCC(F)C(O[Si](C)(C)C)=N1	1389.5	Semi standard non polar	33892256
5,6-Dihydro-5-fluorouracil,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=NCC(F)C(O)=N1	1578.8	Semi standard non polar	33892256
5,6-Dihydro-5-fluorouracil,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1=NC(O)=NCC1F	1559.8	Semi standard non polar	33892256
5,6-Dihydro-5-fluorouracil,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=NCC(F)C(O[Si](C)(C)C(C)(C)C)=N1	1775.3	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 - 5,6-Dihydro-5-fluorouracil GC-MS (Non-derivatized) - 70eV, Positive	splash10-03l0-9300000000-d53f960f30e9f2726fbc	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydro-5-fluorouracil GC-MS (2 TMS) - 70eV, Positive	splash10-0hb9-9440000000-cbbf98d30b677e94205e	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydro-5-fluorouracil GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5,6-Dihydro-5-fluorouracil 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 - 5,6-Dihydro-5-fluorouracil 10V, Positive-QTOF	splash10-001i-1900000000-19ba74a08c9c824e9dc1	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydro-5-fluorouracil 20V, Positive-QTOF	splash10-01q9-5900000000-71963cc6180144de73c6	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydro-5-fluorouracil 40V, Positive-QTOF	splash10-03dm-9000000000-6690c8cc65e6b42ba7ae	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydro-5-fluorouracil 10V, Positive-QTOF	splash10-001i-1900000000-19ba74a08c9c824e9dc1	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydro-5-fluorouracil 20V, Positive-QTOF	splash10-01q9-5900000000-71963cc6180144de73c6	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydro-5-fluorouracil 40V, Positive-QTOF	splash10-03dm-9000000000-6690c8cc65e6b42ba7ae	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydro-5-fluorouracil 10V, Negative-QTOF	splash10-000i-9200000000-07df5cbc1566b0780590	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydro-5-fluorouracil 20V, Negative-QTOF	splash10-0006-9000000000-7125b6d8f066a7df0e7e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5,6-Dihydro-5-fluorouracil 40V, Negative-QTOF	splash10-0006-9000000000-10dcbf73803e32c7e7a7	2016-08-03	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

Cytoplasm

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	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

108825

KEGG Compound ID

C16630

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

121997

PDB ID

Not Available

ChEBI ID

80624

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1795471

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 ]

Enzymes

Enzyme Details

1. Dihydropyrimidinase

General function:: Involved in hydrolase activity
Specific function:: Catalyzes the second step of the reductive pyrimidine degradation, the reversible hydrolytic ring opening of dihydropyrimidines. Can catalyze the ring opening of 5,6-dihydrouracil to N-carbamyl-alanine and of 5,6-dihydrothymine to N-carbamyl-amino isobutyrate.
Gene Name:: DPYS
Uniprot ID:: Q14117
Molecular weight:: 56629.36

Reactions

5,6-Dihydro-5-fluorouracil + Water → alpha-Fluoro-beta-ureidopropionic acid	details

Enzyme Details

2. Dihydropyrimidine dehydrogenase [NADP(+)]

General function:: Involved in electron carrier activity
Specific function:: Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine. Also involved the degradation of the chemotherapeutic drug 5-fluorouracil.
Gene Name:: DPYD
Uniprot ID:: Q12882
Molecular weight:: 111400.32

Reactions

Fluorouracil + NADPH + Hydrogen Ion → 5,6-Dihydro-5-fluorouracil + NADP	details

Showing metabocard for 5,6-Dihydro-5-fluorouracil (HMDB0060402)

MOL for HMDB0060402 (5,6-Dihydro-5-fluorouracil)

3D MOL for HMDB0060402 (5,6-Dihydro-5-fluorouracil)

3D SDF for HMDB0060402 (5,6-Dihydro-5-fluorouracil)

3D-SDF for HMDB0060402 (5,6-Dihydro-5-fluorouracil)

PDB for HMDB0060402 (5,6-Dihydro-5-fluorouracil)

3D PDB for HMDB0060402 (5,6-Dihydro-5-fluorouracil)

SMILES for HMDB0060402 (5,6-Dihydro-5-fluorouracil)

INCHI for HMDB0060402 (5,6-Dihydro-5-fluorouracil)

Structure for HMDB0060402 (5,6-Dihydro-5-fluorouracil)

3D Structure for HMDB0060402 (5,6-Dihydro-5-fluorouracil)

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

Reactions