Cannabis Compound Database: Showing Compound Card for dCDP (CDB004897)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (15) Show 24 proteins XML

Record Information

Version

1.0

Created at

2020-04-17 18:48:09 UTC

Updated at

2020-11-18 16:38:57 UTC

CannabisDB ID

CDB004897

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

dCDP

Description

dCDP, also known as deoxy-CDP, belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O. dCDP is an extremely weak basic (essentially neutral) compound (based on its pKa). dCDP exists in all living species, ranging from bacteria to humans. Within humans, dCDP participates in a number of enzymatic reactions. In particular, dCDP can be biosynthesized from CDP through the action of the enzyme ribonucleoside-diphosphate reductase large subunit. In addition, dCDP can be converted into dCTP; which is mediated by the enzyme nucleoside diphosphate kinase 6. In humans, dCDP is involved in pyrimidine metabolism. Outside of the human body, dCDP has been detected, but not quantified in, several different foods, such as climbing beans, fox grapes, chinese mustards, angelica, and guava. This could make dCDP a potential biomarker for the consumption of these foods. A 2'-deoxycytidine phosphate that is the 2'- deoxy derivative of cytidine 5'-diphosphate (CDP). dCDP 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'-Deoxycytidine 5'-diphosphate	ChEBI
2'-Deoxycytidine diphosphate	ChEBI
D-1beta-Ribofuranosylcytosine diphosphate	ChEBI
Deoxycytidine diphosphate	ChEBI
2'-Deoxycytidine 5'-diphosphoric acid	Generator
2'-Deoxycytidine diphosphoric acid	Generator
D-1b-Ribofuranosylcytosine diphosphate	Generator
D-1b-Ribofuranosylcytosine diphosphoric acid	Generator
D-1beta-Ribofuranosylcytosine diphosphoric acid	Generator
D-1Β-ribofuranosylcytosine diphosphate	Generator
D-1Β-ribofuranosylcytosine diphosphoric acid	Generator
Deoxycytidine diphosphoric acid	Generator
2'-Deoxy-cytidine 5'-pyrophosphate	HMDB
2'-Deoxy-cytidine pyrophosphate	HMDB
2'-Deoxycytidine-5'-diphosphate	HMDB
4-Amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-D-erythro-pentofuranosyl]-2(1H)-pyrimidinone	HMDB
4-Amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-delta-erythro-pentofuranosyl]-2(1H)-pyrimidinone	HMDB
delta-1beta-Ribofuranosylcytosine diphosphate	HMDB
Deoxy-CDP	HMDB
Deoxycytidine 5'-diphosphate	HMDB

Chemical Formula

C₉H₁₅N₃O₁₀P₂

Average Molecular Weight

387.18

Monoisotopic Molecular Weight

387.0233

IUPAC Name

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

Traditional Name

dCDP

CAS Registry Number

800-73-7

SMILES

NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1

InChI Identifier

InChI=1S/C9H15N3O10P2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(21-8)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1

InChI Key

FTDHDKPUHBLBTL-SHYZEUOFSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organic oxoanionic compounds

Sub Class

Organic pyrophosphates

Direct Parent

Organic pyrophosphates

Alternative Parents

Substituents

Organic pyrophosphate
Aminopyrimidine
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Imidolactam
Alkyl phosphate
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Primary amine
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Amine
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine 2'-deoxyribonucleoside 5'-diphosphate (CHEBI:28846 )
2'-deoxycytidine phosphate (CHEBI:28846 )
Deoxyribonucleotides (C00705 )

Ontology

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Plant:

Animal

Biological location:

Subcellular:

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	-1.5	ALOGPS
logP	-2.6	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	1.79	ChemAxon
pKa (Strongest Basic)	0.3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	201.44 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	74.78 m³·mol⁻¹	ChemAxon
Polarizability	30.77 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	dCDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-002e-7912000000-ef0991eaee32b505e016	Spectrum
Predicted GC-MS	dCDP, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0006-9851100000-62426a0730b483cea09b	Spectrum
Predicted GC-MS	dCDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	dCDP, 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	splash10-0570-9418000000-2d9af3073a3dc2deba5d	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - , negative	splash10-056r-9511000000-84defb0c7de79c169ebf	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-000i-0409000000-e5af2ab8466aa7c560d3	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-0a4i-0903000000-1de5fa4ac24e19830f39	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0009000000-4aa3ce1bf37251d7fc83	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-056r-9435000000-55592321586c623c4830	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 30V, Positive	splash10-0a4i-0903000000-1de5fa4ac24e19830f39	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-056r-9411000000-84bbde6c497548c746d1	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-63f9c6b289fb024c58fa	2021-09-20	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-e584f4f2cb1a8a01a7e7	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-3910000000-d34603d21a6d1d52ae1f	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-5900000000-52ac41f181e1d5fbf96a	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000f-4209000000-ea241dab90201ce7963e	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9601000000-55120f468bf1ebba66cd	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-bd81788fb13a599a4f60	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-63028e00ccb9887f46f5	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-1900000000-9b943638c706a10be8db	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-3910000000-f5ebfcca0e4ec5d76afa	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0409000000-47d71d5707b30d7b3ad5	2021-09-25	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9324000000-25bfbc45e3248b83b219	2021-09-25	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-09-25	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
Uridine-cytidine kinase 1	UCK1	9q34.13	Q9HA47	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
Uridine-cytidine kinase 2	UCK2	1q23	Q9BZX2	details
Ribonucleoside-diphosphate reductase subunit M2 B	RRM2B	8q23.1	Q7LG56	details
UMP-CMP kinase 2, mitochondrial	CMPK2	2p25.2	Q5EBM0	details
Uridine-cytidine kinase-like 1	UCKL1	20q13.33	Q9NWZ5	details
Nucleoside diphosphate kinase homolog 5	NME5		P56597	details

Transporters

Not Available

Metal Bindings

Protein Name	Gene Name	Locus	Uniprot ID	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
Ribonucleoside-diphosphate reductase subunit M2 B	RRM2B	8q23.1	Q7LG56	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

HMDB0001245

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB022510

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Deoxycytidine_diphosphate

METLIN ID

6105

PubChem Compound

150855

PDB ID

Not Available

ChEBI ID

28846

References

General References

Not Available

Only showing the first 10 proteins. There are 24 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. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

Enzyme Details

10. Nucleoside diphosphate kinase 6

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. Inhibitor of p53-induced apoptosis.
Gene Name:: NME6
Uniprot ID:: O75414
Molecular weight:: 22002.965

Only showing the first 10 proteins. There are 24 proteins in total.

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Showing Compound Card for dCDP (CDB004897)

Structure for CDB004897 (dCDP)

Enzymes