MiMeDB: Showing metabocard for 5-Thymidylic acid (MMDBc0029594)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:33:40 UTC

Update Date

2024-10-15 19:27:27 UTC

Metabolite ID

MMDBc0029594

Metabolite Identification

Common Name

5-Thymidylic acid

Description

5-Thymidylic acid is a thymine nucleotide. Also known as thymidine monophosphate, and abbreviated TMP, is a nucleotide that is found in DNA. It is an ester of phosphoric acid with the nucleoside thymidine. TMP consists of a phosphate group, esterified to the the pentose sugar deoxyribose moiety, and the nucleobase thymine.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(DT)1	ChEBI
5'-Thymidylic acid	ChEBI
5'-TMP	ChEBI
5-Methyl-dUMP	ChEBI
Deoxyribosylthymine monophosphate	ChEBI
Ribothymidine 5'-monophosphate	ChEBI
Thymidine 5'-(dihydrogen phosphate)	ChEBI
Thymidine 5'-phosphate	ChEBI
Thymidine 5'-phosphoric acid	ChEBI
Thymidine monophosphate	ChEBI
Thymidine-5'-monophosphoric acid	ChEBI
THYMIDINE-5'-phosphATE	ChEBI
Thymidylate	ChEBI
Thymidylic acid	ChEBI
TMP	ChEBI
Deoxythymidine 5'-phosphate	Kegg
Deoxythymidylic acid	Kegg
5'-Thymidylate	Generator
Deoxyribosylthymine monophosphoric acid	Generator
Ribothymidine 5'-monophosphoric acid	Generator
Thymidine 5'-(dihydrogen phosphoric acid)	Generator
Thymidine monophosphoric acid	Generator
Thymidine-5'-monophosphate	Generator
THYMIDINE-5'-phosphoric acid	Generator
Deoxythymidine 5'-phosphoric acid	Generator
Deoxythymidylate	Generator
5-Thymidylate	Generator
2'-Deoxythymidine 5'-monophosphate	HMDB
5'-dTMP	HMDB
Deoxy TMP	HMDB
Deoxythymidine 5'-monophosphate	HMDB
Deoxythymidine monophosphate	HMDB
Deoxythymydilate	HMDB
Deoxythymydilic acid	HMDB
dTMP	HMDB
Thymidine 5'-monophosphate	HMDB
Thymidine 5'-phosphorate	HMDB
Thymidine 5'MP	HMDB
Thymidine mononucleotide	HMDB
Thymidine phosphate	HMDB
Thymidine-5'-monophosphorate	HMDB
Thymidylic acids	HMDB
Acids, thymidylic	HMDB
Acid, thymidylic	HMDB
monoPhosphate, thymidine	HMDB

Molecular Formula

C₁₀H₁₅N₂O₈P

Average Mass

322.2085

Monoisotopic Mass

322.056601978

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

365-07-1

SMILES

Not Available

InChI Identifier

InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1

InChI Key

GYOZYWVXFNDGLU-XLPZGREQSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside monophosphates. These are pyrimidine nucleotides with a monophosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine deoxyribonucleotides

Direct Parent

Pyrimidine 2'-deoxyribonucleoside monophosphates

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside monophosphate
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Lactam
Secondary alcohol
Urea
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxygen compound
Alcohol
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

thymidine 5'-monophosphate (CHEBI:17013 )
Deoxyribonucleotides (C00364 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Not Available

Spectra

Not Available

Biological Properties

Cellular Locations

Lysosome
Mitochondria

Biospecimen Locations

Feces
Fibroblasts

Tissue Locations

Fibroblasts

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191677	5'-nucleotidase	Unknown	P21589	Homo sapiens
MMDBp0191680	Cytosolic 5'-nucleotidase 1B	Unknown	Q96P26	Homo sapiens
MMDBp0191681	Cytosolic 5'-nucleotidase 1A	Unknown	Q9BXI3	Homo sapiens
MMDBp0191682	5'(3')-deoxyribonucleotidase, cytosolic type	Unknown	Q8TCD5	Homo sapiens
MMDBp0191684	5'(3')-deoxyribonucleotidase, mitochondrial	Unknown	Q9NPB1	Homo sapiens
MMDBp0191756	Thymidylate kinase	Enzyme	P23919	Homo sapiens
MMDBp0191757	Ectonucleoside triphosphate diphosphohydrolase 1	Unknown	P49961	Homo sapiens
MMDBp0191758	Soluble calcium-activated nucleotidase 1	Unknown	Q8WVQ1	Homo sapiens
MMDBp0191759	Ectonucleoside triphosphate diphosphohydrolase 3	Unknown	O75355	Homo sapiens
MMDBp0193860	Cytosolic 5'-nucleotidase 3	Enzyme	Q9H0P0	Homo sapiens
MMDBp0193932	Cytosolic purine 5'-nucleotidase	Unknown	P49902	Homo sapiens
MMDBp0193936	Thymidine kinase, cytosolic	Enzyme	P04183	Homo sapiens
MMDBp0193937	Thymidine kinase 2, mitochondrial	Enzyme	O00142	Homo sapiens
MMDBp0193968	Thymidylate synthase	Enzyme	P04818	Homo sapiens
MMDBp0194442	Ectonucleoside triphosphate diphosphohydrolase 8	Unknown	Q5MY95	Homo sapiens
MMDBp0195935	Thymidine kinase	Enzyme	Q8IZR3	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Data Source	Reference
MMDBr0001792	5-Thymidylic acid	Thymidine	acid phosphatase 2, lysosomal	VMH; KEGG	30371894
MMDBr0001793	5-Thymidylic acid	Thymidine	5',3'-nucleotidase, mitochondrial	VMH; KEGG	30371894
MMDBr0002256	Thymidine	5-Thymidylic acid	thymidine kinase 2, mitochondrial	VMH; KEGG	30371894
MMDBr0002573	dTDP	5-Thymidylic acid	ectonucleoside triphosphate diphosphohydrolase 1	VMH; KEGG	30371894
MMDBr0003833	Deoxyadenosine triphosphate	dTDP	Not Available	VMH	8024690
MMDBr0003834	Deoxyadenosine triphosphate	dTDP	Not Available	VMH	8024690
MMDBr0005451	5-Thymidylic acid	dTDP	deoxythymidylate kinase (thymidylate kinase)	VMH; KEGG	30371894
MMDBr0006995	Thymidine 5'-triphosphate	5-Thymidylic acid	Not Available	VMH	30371894
MMDBr0007323	5-Thymidylic acid	dTDP	Not Available	VMH; KEGG	30371894
MMDBr0007580	Thymidine	5-Thymidylic acid	Not Available	VMH; KEGG	30371894
MMDBr0007639	5-Thymidylic acid	Thymidine	Not Available	VMH; KEGG	30371894
MMDBr0007980	dUMP	Dihydrofolic acid	Not Available	VMH; KEGG	30371894
MMDBr0008126	dUMP	5-Thymidylic acid	Not Available	VMH	30371894
MMDBr0008412	Guanosine triphosphate	5-Thymidylic acid	Not Available	VMH	30371894
MMDBr0011016	dUMP	5-Thymidylic acid	Not Available	VMH	30371894

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	547	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Cattle ; River trout ; Rat ; Sheep ; Chicken ; Dog ; Lion ; American dog tick ; Turkey	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	517	Human feces; Human pleural fluid plaque; Pig ; Human sputum; Human ; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Human supragingival plaque; Cattle ; Human stool; Catfish	Metabolic reconstruction
Bacteria	Actinobacteria	165	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva; Cattle	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	133	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human subgingival plaque; Human supragingival plaque; Human urine	Metabolic reconstruction
Bacteria	Synergistetes	5	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	11	Human feces; Pig ; Human	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	6		Metabolic reconstruction
Bacteria	Candidatus melainabacteria	1	Human feces	Metabolic reconstruction
Bacteria	Tenericutes	26	Human feces; Human ; Goat ; Pig	Metabolic reconstruction
Bacteria	Planctomycetes	2	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Viruses/Bamfordvirae	Nucleocytoviricota	32
Viruses/Heunggongvirae	Uroviricota	6
Eukaryota/Fungi	Microsporidia	1
Eukaryota/Fungi	Basidiomycota	3	Human feces
Eukaryota/Fungi	Ascomycota	5	Human feces; Human saliva	Unknown
Bacteria	Deinococcus-thermus	5
Viruses/Heunggongvirae	Peploviricota	17	Human saliva
Viruses	nah	1
Bacteria	Cyanobacteria	28
Archaea/Archaea	Crenarchaeota	8		Metabolic reconstruction
Bacteria	Aquificae	2
Archaea/Archaea	Euryarchaeota	33		Metabolic reconstruction
Bacteria	Chlamydiae	10	Human ; Sheep ; Cat
Bacteria	Chlorobi	9
Bacteria	Chloroflexi	10
Bacteria	Thermotogae	9
Bacteria	nah	1
Viruses	Peploviricota	20	Human saliva
Bacteria	Dictyoglomi	2
Bacteria	Elusimicrobia	1
Bacteria	Acidobacteria	1

Exposure Sources

Source Type	Source Sub-type	Source Name	Data Source	Reference

Source Type	Activity	Data Source	Reference
Drugs	Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	Not Available	U.S. Environmental Protection Agency	CompTox
Domestics	Not Available	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified				HMDB
Human Fibroblasts	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	25037050

External Links

HMDB ID

HMDB0001227

DrugBank ID

DB01643

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Thymidine_monophosphate

METLIN ID

6092

PubChem Compound

9700

PDB ID

Not Available

ChEBI ID

17013

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Terai C, Carson DA: Pyrimidine nucleotide and nucleic acid synthesis in human monocytes and macrophages. Exp Cell Res. 1991 Apr;193(2):375-81. doi: 10.1016/0014-4827(91)90110-g. [PubMed:1706277 ]
Seno T, Ayusawa D, Shimizu K, Koyama H, Takeishi K, Hori T: Thymineless death and genetic events in mammalian cells. Basic Life Sci. 1985;31:241-63. doi: 10.1007/978-1-4613-2449-2_15. [PubMed:3888175 ]
Gribaudo G, Riera L, Lembo D, De Andrea M, Gariglio M, Rudge TL, Johnson LF, Landolfo S: Murine cytomegalovirus stimulates cellular thymidylate synthase gene expression in quiescent cells and requires the enzyme for replication. J Virol. 2000 Jun;74(11):4979-87. doi: 10.1128/jvi.74.11.4979-4987.2000. [PubMed:10799571 ]
Gribaudo G, Riera L, Caposio P, Maley F, Landolfo S: Human cytomegalovirus requires cellular deoxycytidylate deaminase for replication in quiescent cells. J Gen Virol. 2003 Jun;84(Pt 6):1437-1441. doi: 10.1099/vir.0.18979-0. [PubMed:12771412 ]

Showing metabocard for 5-Thymidylic acid (MMDBc0029594)

MOL for #<Metabolite:0x00007fb7e8fdc4e0>

3D MOL for #<Metabolite:0x00007fb7e8fdc4e0>

3D SDF for #<Metabolite:0x00007fb7e8fdc4e0>

3D-SDF for #<Metabolite:0x00007fb7e8fdc4e0>

PDB for #<Metabolite:0x00007fb7e8fdc4e0>

3D PDB for #<Metabolite:0x00007fb7e8fdc4e0>

SMILES for #<Metabolite:0x00007fb7e8fdc4e0>

INCHI for #<Metabolite:0x00007fb7e8fdc4e0>

Structure for #<Metabolite:0x00007fb7e8fdc4e0>

3D Structure for #<Metabolite:0x00007fb7e8fdc4e0>