Cannabis Compound Database: Showing Compound Card for CDP (CDB005322)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (30) Show 46 proteins XML

Record Information

Version

1.0

Created at

2020-04-17 19:31:35 UTC

Updated at

2020-11-18 16:39:43 UTC

CannabisDB ID

CDB005322

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

CDP

Description

CDP, also known as 5'-CDP, belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. A cytosine nucleotide containing two phosphate groups esterified to the sugar moiety. CDP is an extremely weak basic (essentially neutral) compound (based on its pKa). CDP exists in all living species, ranging from bacteria to humans. In humans, CDP is involved in cardiolipin biosynthesis. Outside of the human body, CDP has been detected, but not quantified in, several different foods, such as carobs, mexican oregano, evergreen huckleberries, green vegetables, and pepper (c. baccatum). This could make CDP a potential biomarker for the consumption of these foods. CDP is expected to be in Cannabis as all living plants are known to produce and metabolize it.

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

Value	Source
5'-CDP	ChEBI
Cytidine 5'-diphosphate	ChEBI
Cytidine 5'-diphosphoric acid	ChEBI
Cytidine 5'-pyrophosphate	ChEBI
Cytidine diphosphate	ChEBI
Cytidine, 5'-(trihydrogen pyrophosphate)	ChEBI
CYTIDINE-5'-diphosphATE	ChEBI
Cytidine 5'-pyrophosphoric acid	Generator
Cytidine diphosphoric acid	Generator
Cytidine, 5'-(trihydrogen pyrophosphoric acid)	Generator
CYTIDINE-5'-diphosphoric acid	Generator
Cytidine-diphosphate	HMDB
Diphosphate, cytidine	HMDB

Chemical Formula

C₉H₁₅N₃O₁₁P₂

Average Molecular Weight

403.18

Monoisotopic Molecular Weight

403.0182

IUPAC Name

[({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional Name

CDP

CAS Registry Number

63-38-7

SMILES

NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

InChI Key

ZWIADYZPOWUWEW-XVFCMESISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine ribonucleotides

Direct Parent

Pyrimidine ribonucleoside diphosphates

Alternative Parents

Substituents

Pyrimidine ribonucleoside diphosphate
Pentose-5-phosphate
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Pentose monosaccharide
Organic pyrophosphate
Monosaccharide phosphate
Monoalkyl phosphate
Pyrimidone
Aminopyrimidine
Imidolactam
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
Monosaccharide
Hydropyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

cytidine 5'-phosphate (CHEBI:17239 )
pyrimidine ribonucleoside 5'-diphosphate (CHEBI:17239 )
Ribonucleotides (C00112 )

Ontology

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Plant:

Animal

Biological location:

Biofluid and excreta:

Blood

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	2.44	HANSCH,C ET AL. (1995)

Predicted Properties

Property	Value	Source
logP	-1.4	ALOGPS
logP	-3.3	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.78	ChemAxon
pKa (Strongest Basic)	-0.033	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	221.67 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	76.29 m³·mol⁻¹	ChemAxon
Polarizability	31.39 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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	CDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-004i-5923000000-f7e7b227d8dab9e29e4b	Spectrum
Predicted GC-MS	CDP, 2 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-00di-3209010000-ff27ee45250db3e35193	Spectrum
Predicted GC-MS	CDP, 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-ITFT , negative	splash10-004i-9000000000-f5d958a3ccf576052a6b	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-00di-0390000000-0274cdf4190792442001	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-0udi-0009000000-2c8a9272dc29076a6167	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-0kdi-9602700000-4b46ddc9506634a02dc5	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , positive	splash10-0a4i-0059000000-d598d99a604dda402181	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-0udi-0003900000-69398917fb0c37a4304f	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-0zg0-0726900000-8d967e8ca6677a467fb8	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - 30V, Positive	splash10-0k9i-0927400000-86e5ba01091f928ca88f	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0kdi-9814400000-54042f12a186a46a5a17	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 30V, Positive	splash10-0k9i-0927400000-61338365caaf6cc96edd	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-03di-0900000000-2e5da7181d5154fd5287	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 30V, Negative	splash10-056r-8913200000-d327869c80aa6b6ba8b7	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 30V, Negative	splash10-056r-7913200000-4f2656e2010a4274c652	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9200000000-ae7cefa275aa112f8ff3	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0000900000-1f74a916c1bec3408d2e	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-056r-9601000000-0261d005e8d3964fc255	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 30V, Negative	splash10-056r-8913200000-3093e23d54c628f19ea0	2021-09-20	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0901000000-6aed044cc4135aa261df	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-3900000000-92fac6a8baf47bac3014	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-5900000000-5ad7bca4dc732a0e3840	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-0903300000-44d24cfda26f8f0a8d96	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9701000000-d96a23308bcfcf9cf55f	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-d7e0d2a5e8d20180b483	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0100900000-fd8a10c051d8566d4abc	2021-09-23	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-056r-9418200000-cd847d00773e220445dd	2021-09-23	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
UMP-CMP kinase	CMPK1	1p32	P30085	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
Nucleoside diphosphate kinase, mitochondrial	NME4	16p13.3	O00746	details
Ribonucleoside-diphosphate reductase large subunit	RRM1	11p15.5	P23921	details
Nucleoside diphosphate kinase A	NME1	17q21.3	P15531	details
Nucleoside diphosphate kinase 7	NME7	1q24	Q9Y5B8	details
Ribonucleoside-diphosphate reductase subunit M2	RRM2	2p25-p24	P31350	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
6-phosphofructokinase type C	PFKP	10p15.3-p15.2	Q01813	details
6-phosphofructokinase, liver type	PFKL	21q22.3	P17858	details
6-phosphofructokinase, muscle type	PFKM	12q13.3	P08237	details
Pyruvate kinase isozymes M1/M2	PKM	15q22	P14618	details
Pyruvate kinase isozymes R/L	PKLR	1q21	P30613	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
Polyribonucleotide nucleotidyltransferase 1, mitochondrial	PNPT1	2p15	Q8TCS8	details
Ribonucleoside-diphosphate reductase subunit M2 B	RRM2B	8q23.1	Q7LG56	details
UMP-CMP kinase 2, mitochondrial	CMPK2	2p25.2	Q5EBM0	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
Dolichol kinase	DOLK	9q34.11	Q9UPQ8	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
Ribonucleoside-diphosphate reductase subunit M2	RRM2	2p25-p24	P31350	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
6-phosphofructokinase type C	PFKP	10p15.3-p15.2	Q01813	details
6-phosphofructokinase, liver type	PFKL	21q22.3	P17858	details
6-phosphofructokinase, muscle type	PFKM	12q13.3	P08237	details
Pyruvate kinase isozymes M1/M2	PKM	15q22	P14618	details
Pyruvate kinase isozymes R/L	PKLR	1q21	P30613	details
Ribonucleoside-diphosphate reductase subunit M2 B	RRM2B	8q23.1	Q7LG56	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
Ribonucleoside-diphosphate reductase subunit M2	RRM2	2p25-p24	P31350	details
Nucleoside diphosphate kinase B	NME2	17q21.3	P22392	details

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0001546

DrugBank ID

DB04555

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB022683

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

17239

References

General References

Not Available

Only showing the first 10 proteins. There are 46 proteins in total.

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Enzymes

Enzyme Details

1. UMP-CMP kinase

General function:: Involved in ATP binding
Specific function:: Catalyzes specific phosphoryl transfer from ATP to UMP and CMP.
Gene Name:: CMPK1
Uniprot ID:: P30085
Molecular weight:: 20180.12

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. 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

6. Ribonucleoside-diphosphate reductase large subunit

General function:: Involved in oxidation reduction
Specific function:: Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.
Gene Name:: RRM1
Uniprot ID:: P23921
Molecular weight:: 90069.375

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. Ribonucleoside-diphosphate reductase subunit M2

General function:: Involved in oxidoreductase activity
Specific function:: Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. Inhibits Wnt signaling.
Gene Name:: RRM2
Uniprot ID:: P31350
Molecular weight:: 44877.25

Enzyme Details

10. 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

Only showing the first 10 proteins. There are 46 proteins in total.

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Showing Compound Card for CDP (CDB005322)

Structure for CDB005322 (CDP)

Enzymes