Cannabis Compound Database: Showing Compound Card for dTDP (CDB004904)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (24) Show 32 proteins XML

Record Information

Version

1.0

Created at

2020-04-17 18:48:54 UTC

Updated at

2020-11-18 16:38:58 UTC

CannabisDB ID

CDB004904

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

dTDP

Description

dTDP, also known as deoxy-TDP, belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside diphosphates. These are pyrimidine nucleotides with a diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. dTDP is an extremely weak basic (essentially neutral) compound (based on its pKa). dTDP exists in all living species, ranging from bacteria to humans. Outside of the human body, dTDP has been detected, but not quantified in, several different foods, such as brussel sprouts, wheats, herbs and spices, papaya, and red raspberries. This could make dTDP a potential biomarker for the consumption of these foods. A thymidine phosphate having a diphosphate group at the 5'-position. dTDP 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
2'-Deoxyribosylthymine 5'-(trihydrogen diphosphate)	ChEBI
Deoxy-TDP	ChEBI
Deoxythymidine 5'-diphosphate	ChEBI
Thymidine 5'-diphosphate	ChEBI
Thymidine 5'-pyrophosphate	ChEBI
THYMIDINE-5'- diphosphATE	ChEBI
2'-Deoxyribosylthymine 5'-(trihydrogen diphosphoric acid)	Generator
Deoxythymidine 5'-diphosphoric acid	Generator
Thymidine 5'-diphosphoric acid	Generator
Thymidine 5'-pyrophosphoric acid	Generator
THYMIDINE-5'- diphosphoric acid	Generator
TDP	HMDB

Chemical Formula

C₁₀H₁₆N₂O₁₁P₂

Average Molecular Weight

402.19

Monoisotopic Molecular Weight

402.0229

IUPAC Name

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

Traditional Name

dTDP

CAS Registry Number

491-97-4

SMILES

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

InChI Identifier

InChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1

InChI Key

UJLXYODCHAELLY-XLPZGREQSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside diphosphates. These are pyrimidine nucleotides with a diphosphate 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 diphosphates

Alternative Parents

Substituents

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

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine 2'-deoxyribonucleoside 5'-diphosphate (CHEBI:18075 )
thymidine phosphate (CHEBI:18075 )
Deoxyribonucleotides (C00363 )

Ontology

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Plant:

Animal

Biological location:

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	-0.87	ALOGPS
logP	-1.7	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	192.16 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	77.16 m³·mol⁻¹	ChemAxon
Polarizability	32.12 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
Predicted GC-MS	dTDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-004m-6922000000-78987adf8e4b2b4baa77	Spectrum
Predicted GC-MS	dTDP, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-00dm-9341200000-af3e3a557688731137d2	Spectrum
Predicted GC-MS	dTDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-0kdi-9720700000-003f87d03143415a6bf9	2017-09-14	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-f02dc55e07c9935275d9	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-4901000000-bc16523808594ec9a806	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-5900000000-2199218952cf36a3e3a2	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-2607900000-696f76b41235895dc296	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9801000000-9bc55b2280dfcf3aed1d	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-d33e29452de0777eaa0d	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-1100900000-bedafc8a6d3579ef1476	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9102100000-8cad78608dae5988a8c1	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-0ff3218786dbaaac7dea	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0920500000-ccf96f505a327015ed67	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-2910000000-857f636dcd89f8378f36	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-2910000000-b95a62414e3f309b00bb	2021-09-24	View Spectrum

NMR

Not Available

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
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
Uridine-cytidine kinase 1	UCK1	9q34.13	Q9HA47	details
Nucleoside diphosphate kinase, mitochondrial	NME4	16p13.3	O00746	details
Nucleoside diphosphate kinase A	NME1	17q21.3	P15531	details
Nucleoside diphosphate kinase 7	NME7	1q24	Q9Y5B8	details
Nucleoside diphosphate kinase B	NME2	17q21.3	P22392	details
Nucleoside diphosphate kinase 3	NME3	16q13.3	Q13232	details
Nucleoside diphosphate kinase 6	NME6	3p21	O75414	details
Ectonucleoside triphosphate diphosphohydrolase 4	ENTPD4	8p21.3	Q9Y227	details
Ectonucleoside triphosphate diphosphohydrolase 6	ENTPD6	20p11.21	O75354	details
Ectonucleoside triphosphate diphosphohydrolase 5	ENTPD5	14q24	O75356	details
dTDP-D-glucose 4,6-dehydratase	TGDS	13q32.1	O95455	details
Polyribonucleotide nucleotidyltransferase 1, mitochondrial	PNPT1	2p15	Q8TCS8	details
Uridine-cytidine kinase 2	UCK2	1q23	Q9BZX2	details
Uridine-cytidine kinase-like 1	UCKL1	20q13.33	Q9NWZ5	details
Ectonucleoside triphosphate diphosphohydrolase 8	ENTPD8	9q34.3	Q5MY95	details
Putative nucleoside diphosphate kinase	NME2P1	12q24.31	O60361	details
Probable 8-oxo-dGTP diphosphatase NUDT15	NUDT15	13q14.2	Q9NV35	details
8-oxo-dGDP phosphatase NUDT18	NUDT18	8p21.3	Q6ZVK8	details
Nucleoside diphosphate kinase	NME4	16p13.3	A2IDD0	details
Nucleoside diphosphate kinase homolog 5	NME5		P56597	details

Transporters

Not Available

Metal Bindings

Protein Name	Gene Name	Locus	Uniprot ID	Details
Soluble calcium-activated nucleotidase 1	CANT1	17q25.3	Q8WVQ1	details
Nucleoside diphosphate kinase, mitochondrial	NME4	16p13.3	O00746	details
Nucleoside diphosphate kinase 7	NME7	1q24	Q9Y5B8	details
Nucleoside diphosphate kinase B	NME2	17q21.3	P22392	details
Nucleoside diphosphate kinase 3	NME3	16q13.3	Q13232	details
Nucleoside diphosphate kinase 6	NME6	3p21	O75414	details
Probable 8-oxo-dGTP diphosphatase NUDT15	NUDT15	13q14.2	Q9NV35	details

Receptors

Not Available

Transcriptional Factors

Protein Name	Gene Name	Locus	Uniprot ID	Details
Nucleoside diphosphate kinase B	NME2	17q21.3	P22392	details

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0001274

DrugBank ID

DB03103

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Thymidine_diphosphate

METLIN ID

6129

PubChem Compound

164628

PDB ID

Not Available

ChEBI ID

18075

References

General References

Not Available

Only showing the first 10 proteins. There are 32 proteins in total.

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Enzymes

Enzyme Details

1. 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

2. 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

3. 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

4. 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

5. Uridine-cytidine kinase 1

General function:: Involved in ATP binding
Specific function:: Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
Gene Name:: UCK1
Uniprot ID:: Q9HA47
Molecular weight:: 22760.43

Enzyme Details

6. Nucleoside diphosphate kinase, mitochondrial

General function:: Involved in nucleoside diphosphate kinase activity
Specific function:: Major role in the synthesis of nucleoside triphosphates other than ATP (By similarity).
Gene Name:: NME4
Uniprot ID:: O00746
Molecular weight:: 20658.45

Enzyme Details

7. Nucleoside diphosphate kinase A

General function:: Involved in nucleoside diphosphate kinase activity
Specific function:: Major role in the synthesis of nucleoside triphosphates other than ATP. Possesses nucleoside-diphosphate kinase, serine/threonine-specific protein kinase, geranyl and farnesyl pyrophosphate kinase, histidine protein kinase and 3'-5' exonuclease activities. Involved in cell proliferation, differentiation and development, signal transduction, G protein-coupled receptor endocytosis, and gene expression. Required for neural development including neural patterning and cell fate determination.
Gene Name:: NME1
Uniprot ID:: P15531
Molecular weight:: 17148.635

Enzyme Details

8. Nucleoside diphosphate kinase 7

General function:: Involved in nucleoside diphosphate kinase activity
Specific function:: Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate.
Gene Name:: NME7
Uniprot ID:: Q9Y5B8
Molecular weight:: 42491.365

Enzyme Details

9. Nucleoside diphosphate kinase B

General function:: Involved in nucleoside diphosphate kinase activity
Specific function:: Major role in the synthesis of nucleoside triphosphates other than ATP. Negatively regulates Rho activity by interacting with AKAP13/LBC. Acts as a transcriptional activator of the MYC gene; binds DNA non-specifically (PubMed:8392752). Exhibits histidine protein kinase activity.
Gene Name:: NME2
Uniprot ID:: P22392
Molecular weight:: 30136.92

Enzyme Details

10. Nucleoside diphosphate kinase 3

General function:: Involved in nucleoside diphosphate kinase activity
Specific function:: Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Probably has a role in normal hematopoiesis by inhibition of granulocyte differentiation and induction of apoptosis.
Gene Name:: NME3
Uniprot ID:: Q13232
Molecular weight:: 19014.85

Only showing the first 10 proteins. There are 32 proteins in total.

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Showing Compound Card for dTDP (CDB004904)

Structure for CDB004904 (dTDP)

Enzymes