Cannabis Compound Database: Showing Compound Card for 5-Thymidylic acid (CDB005247)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (16) Show 26 proteins XML

Record Information

Version

1.0

Created at

2020-04-17 19:24:04 UTC

Updated at

2020-11-18 16:39:36 UTC

CannabisDB ID

CDB005247

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

5-Thymidylic acid

Description

5-Thymidylic acid, also known as TMP or thymidylate, 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. 5-Thymidylic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). The neutral species of 5-Thymidylic acid (2'-deoxythymidine 5'-monophosphate). 5-Thymidylic acid exists in all living species, ranging from bacteria to humans. Within humans, 5-thymidylic acid participates in a number of enzymatic reactions. In particular, 5-thymidylic acid and dihydrofolic acid can be biosynthesized from dUMP and 5,10-methylene-THF; which is mediated by the enzyme thymidylate synthase. In addition, 5-thymidylic acid can be converted into dTDP; which is catalyzed by the enzyme thymidylate synthase. In humans, 5-thymidylic acid is involved in pyrimidine metabolism. Outside of the human body, 5-Thymidylic acid has been detected, but not quantified in, several different foods, such as common buckwheats, corn salad, garden cress, squashberries, and star fruits. This could make 5-thymidylic acid a potential biomarker for the consumption of these foods. 5-Thymidylic acid is expected to be in Cannabis as all living plants are known to produce and metabolize it.

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

Chemical Formula

C₁₀H₁₅N₂O₈P

Average Molecular Weight

322.21

Monoisotopic Molecular Weight

322.0566

IUPAC Name

{[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy}phosphonic acid

Traditional Name

thymidylate

CAS Registry Number

365-07-1

SMILES

CC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(O)=O)O2)C(=O)NC1=O

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 )

Ontology

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Plant:

Animal

Biological location:

Cell and elements:

Cell:

Fibroblast

Biofluid and excreta:

Feces

Subcellular:

Role

Industrial application:

Pharmaceutical industry:

Pharmaceutical

Physical Properties

State

Solid

Experimental 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

Predicted Properties

Property	Value	Source
logP	-1.4	ALOGPS
logP	-1.2	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	145.63 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	66.28 m³·mol⁻¹	ChemAxon
Polarizability	27.46 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
GC-MS	5-Thymidylic acid, non-derivatized, GC-MS Spectrum	splash10-01u0-0961000000-4380a23f8bec3c2dd015	Spectrum
GC-MS	5-Thymidylic acid, non-derivatized, GC-MS Spectrum	splash10-03k9-0940000000-6238904f1b1f293aaf3a	Spectrum
GC-MS	5-Thymidylic acid, non-derivatized, GC-MS Spectrum	splash10-01u0-0961000000-4380a23f8bec3c2dd015	Spectrum
GC-MS	5-Thymidylic acid, non-derivatized, GC-MS Spectrum	splash10-03k9-0940000000-6238904f1b1f293aaf3a	Spectrum
Predicted GC-MS	5-Thymidylic acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0002-9500000000-ca4d82d816839360b115	Spectrum
Predicted GC-MS	5-Thymidylic acid, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0002-9621000000-1a0c588cd8f192b77565	Spectrum
Predicted GC-MS	5-Thymidylic acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	5-Thymidylic acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-001i-9110000000-a45c0d5a58cdb0e5fee4	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-001i-9000000000-624fe22ca203d0e6430e	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-001i-9000000000-0c23943cc868acaaeda4	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-004i-9703000000-452b674ca61adb40209b	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-004i-9703000000-452b674ca61adb40209b	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9000000000-2233c579a23110abe895	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9000000000-9af792986db292f0d8d1	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-001i-9010000000-9936ff7b595382418b7c	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9200000000-5c7a9e2c6c970eec2d92	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9000000000-edfd7498bf3ebaedbb4b	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-001i-9000000000-9dafb0586b1aadb8475d	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-001i-9100000000-b286ae95b38725486f5b	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9000000000-c716e9bc2009f1adb3ae	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-ec3ffc3673cc769d3a0e	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-004i-8900000000-90b7e520ce562f39a280	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-004i-7900000000-a01024a3e21d2de7f133	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-004j-5900000000-57620f7a2b0abf78c220	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-004i-8900000000-b0b0ac82c08ccb2ea84e	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-006t-0905000000-49f5a9d8a112c369032d	2021-09-20	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-b932c025cbc139ba930b	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-4900000000-ae144ce0df705b85f237	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-5900000000-9f2e5ba96fb24ff28b7f	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-9766000000-855dcb81a8d160218e77	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9200000000-f9116de370dd3211ece6	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-0953b010bfa0e123afa7	2016-09-12	View Spectrum

NMR

Type	Description	View
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Spectrum
1D NMR	¹H NMR Spectrum (1D, D₂O, experimental)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
2D NMR	[¹H, ¹H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)	Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Spectrum

Pathways

Name	SMPDB/Pathwhiz	KEGG
Pyrimidine Metabolism
Beta Ureidopropionase Deficiency		Not Available
UMP Synthase Deficiency (Orotic Aciduria)		Not Available
Dihydropyrimidinase Deficiency		Not Available
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)		Not Available

Protein Targets

Enzymes

Protein Name	Gene Name	Locus	Uniprot ID	Details
5'-nucleotidase	NT5E	6q14-q21	P21589	details
Cytosolic 5'-nucleotidase 1B	NT5C1B	2p24.2	Q96P26	details
Cytosolic 5'-nucleotidase 1A	NT5C1A	1p34.3-p33	Q9BXI3	details
5'(3')-deoxyribonucleotidase, cytosolic type	NT5C		Q8TCD5	details
5'(3')-deoxyribonucleotidase, mitochondrial	NT5M		Q9NPB1	details
Thymidylate kinase	DTYMK	2q37.3	P23919	details
Ectonucleoside triphosphate diphosphohydrolase 1	ENTPD1	10q24	P49961	details
Soluble calcium-activated nucleotidase 1	CANT1	17q25.3	Q8WVQ1	details
Ectonucleoside triphosphate diphosphohydrolase 3	ENTPD3	3p21.3	O75355	details
Cytosolic 5'-nucleotidase 3	NT5C3	7p14.3	Q9H0P0	details
Cytosolic purine 5'-nucleotidase	NT5C2	10q24.32	P49902	details
Thymidine kinase, cytosolic	TK1	17q23.2-q25.3	P04183	details
Thymidine kinase 2, mitochondrial	TK2	16q22-q23.1	O00142	details
Thymidylate synthase	TYMS	18p11.32	P04818	details
Ectonucleoside triphosphate diphosphohydrolase 8	ENTPD8	9q34.3	Q5MY95	details
Thymidine kinase			Q8IZR3	details

Transporters

Not Available

Metal Bindings

Protein Name	Gene Name	Locus	Uniprot ID	Details
5'-nucleotidase	NT5E	6q14-q21	P21589	details
Cytosolic 5'-nucleotidase 1B	NT5C1B	2p24.2	Q96P26	details
Cytosolic 5'-nucleotidase 1A	NT5C1A	1p34.3-p33	Q9BXI3	details
5'(3')-deoxyribonucleotidase, cytosolic type	NT5C		Q8TCD5	details
5'(3')-deoxyribonucleotidase, mitochondrial	NT5M		Q9NPB1	details
Soluble calcium-activated nucleotidase 1	CANT1	17q25.3	Q8WVQ1	details
Cytosolic 5'-nucleotidase 3	NT5C3	7p14.3	Q9H0P0	details
Cytosolic purine 5'-nucleotidase	NT5C2	10q24.32	P49902	details
Thymidine kinase, cytosolic	TK1	17q23.2-q25.3	P04183	details

Receptors

Not Available

Transcriptional Factors

Protein Name	Gene Name	Locus	Uniprot ID	Details
Thymidylate synthase	TYMS	18p11.32	P04818	details

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0001227

DrugBank ID

DB01643

Phenol Explorer Compound ID

Not Available

FoodDB 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

References

General References

Not Available

Only showing the first 10 proteins. There are 26 proteins in total.

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Enzymes

Enzyme Details

1. 5'-nucleotidase

General function:: Involved in hydrolase activity
Specific function:: Hydrolyzes extracellular nucleotides into membrane permeable nucleosides.
Gene Name:: NT5E
Uniprot ID:: P21589
Molecular weight:: 57948.125

Enzyme Details

2. Cytosolic 5'-nucleotidase 1B

General function:: Involved in nucleotide binding
Specific function:: Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides. Helps to regulate adenosine levels (By similarity).
Gene Name:: NT5C1B
Uniprot ID:: Q96P26
Molecular weight:: 68803.055

Enzyme Details

3. Cytosolic 5'-nucleotidase 1A

General function:: Involved in nucleotide binding
Specific function:: Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides and has a broad substrate specificity. Helps to regulate adenosine levels in heart during ischemia and hypoxia.
Gene Name:: NT5C1A
Uniprot ID:: Q9BXI3
Molecular weight:: 41020.145

Enzyme Details

4. 5'(3')-deoxyribonucleotidase, cytosolic type

General function:: Involved in metal ion binding
Specific function:: Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides, with a preference for dUMP and dTMP, intermediate activity towards dGMP, and low activity towards dCMP and dAMP.
Gene Name:: NT5C
Uniprot ID:: Q8TCD5
Molecular weight:: Not Available

Enzyme Details

5. 5'(3')-deoxyribonucleotidase, mitochondrial

General function:: Involved in phosphatase activity
Specific function:: Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
Gene Name:: NT5M
Uniprot ID:: Q9NPB1
Molecular weight:: Not Available

Enzyme Details

6. Thymidylate kinase

General function:: Involved in thymidylate kinase activity
Specific function:: Catalyzes the conversion of dTMP to dTDP.
Gene Name:: DTYMK
Uniprot ID:: P23919
Molecular weight:: 23819.105

Enzyme Details

7. Ectonucleoside triphosphate diphosphohydrolase 1

General function:: Involved in hydrolase activity
Specific function:: In the nervous system, could hydrolyze ATP and other nucleotides to regulate purinergic neurotransmission. Could also be implicated in the prevention of platelet aggregation by hydrolyzing platelet-activating ADP to AMP. Hydrolyzes ATP and ADP equally well.
Gene Name:: ENTPD1
Uniprot ID:: P49961
Molecular weight:: 58706.0

Enzyme Details

8. Soluble calcium-activated nucleotidase 1

General function:: Involved in calcium ion binding
Specific function:: Calcium-dependent nucleotidase with a preference for UDP. The order of activity with different substrates is UDP > GDP > UTP > GTP. Has very low activity towards ADP and even lower activity towards ATP. Does not hydrolyze AMP and GMP. Involved in proteoglycan synthesis.
Gene Name:: CANT1
Uniprot ID:: Q8WVQ1
Molecular weight:: 44839.24

Enzyme Details

9. Ectonucleoside triphosphate diphosphohydrolase 3

General function:: Involved in hydrolase activity
Specific function:: Has a threefold preference for the hydrolysis of ATP over ADP.
Gene Name:: ENTPD3
Uniprot ID:: O75355
Molecular weight:: 59104.76

Enzyme Details

10. Cytosolic 5'-nucleotidase 3

General function:: Involved in magnesium ion binding
Specific function:: Can act both as nucleotidase and as phosphotransferase.
Gene Name:: NT5C3
Uniprot ID:: Q9H0P0
Molecular weight:: 33914.91

Only showing the first 10 proteins. There are 26 proteins in total.

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Showing Compound Card for 5-Thymidylic acid (CDB005247)

Structure for CDB005247 (5-Thymidylic acid)

Enzymes