Cannabis Compound Database: Showing Compound Card for Deoxycytidine (CDB004782)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (11) Show 22 proteins XML

Record Information

Version

1.0

Created at

2020-04-17 18:36:13 UTC

Updated at

2020-11-18 16:38:40 UTC

CannabisDB ID

CDB004782

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

Deoxycytidine

Description

Deoxycytidine, also known as dC, belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. Deoxycytidine is an extremely weak basic (essentially neutral) compound (based on its pKa). Deoxycytidine exists in all living species, ranging from bacteria to humans. Within humans, deoxycytidine participates in a number of enzymatic reactions. In particular, deoxycytidine can be biosynthesized from dCMP; which is mediated by the enzyme cytosolic purine 5'-nucleotidase. In addition, deoxycytidine can be converted into dCMP through its interaction with the enzyme uridine-cytidine kinase-like 1. In humans, deoxycytidine is involved in the metabolic disorder called the beta-ureidopropionase deficiency pathway. Outside of the human body, Deoxycytidine has been detected, but not quantified in, several different foods, such as common sages, greenthread tea, chinese broccoli, oil palms, and lingonberries. This could make deoxycytidine a potential biomarker for the consumption of these foods. A pyrimidine 2'-deoxyribonucleoside having cytosine as the nucleobase. Deoxycytidine 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
4-Amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidin-2(1H)-one	ChEBI
dC	ChEBI
DCYD	ChEBI
2'-Deoxycytidine	Kegg
1-(2-Deoxy-b-D-ribofuranosyl)cytosine	HMDB
1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-cytosine	HMDB
1-(2-Deoxy-beta-D-ribofuranosyl)cytosine	HMDB
1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-cytosine	HMDB
1-(2-Deoxy-beta-delta-ribofuranosyl)cytosine	HMDB
2-Deoxy-cytidine	HMDB
4-Amino-1-(2-deoxy-b-D-erythro-pentofuranosyl)-2(1H)-pyrimidinone	HMDB
4-Amino-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-2(1H)-pyrimidinone	HMDB
4-Amino-1-(2-deoxy-beta-delta-erythro-pentofuranosyl)-2(1H)-pyrimidinone	HMDB
Cytosine deoxyribonucleoside	HMDB
Cytosine deoxyriboside	HMDB
Deoxy-cytidine	HMDB
Deoxyribose cytidine	HMDB
Desoxycytidine	HMDB
Deoxyribonucleoside, cytosine	HMDB
Deoxyriboside, cytosine	HMDB
Deoxycytidine	ChEBI

Chemical Formula

C₉H₁₃N₃O₄

Average Molecular Weight

227.22

Monoisotopic Molecular Weight

227.0906

IUPAC Name

4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

Traditional Name

2'-deoxycytidine

CAS Registry Number

951-77-9

SMILES

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

InChI Identifier

InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)/t5-,6+,8+/m0/s1

InChI Key

CKTSBUTUHBMZGZ-SHYZEUOFSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2'-deoxyribonucleosides

Direct Parent

Pyrimidine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside
Aminopyrimidine
Pyrimidone
Hydropyrimidine
Pyrimidine
Imidolactam
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Azacycle
Oxacycle
Organoheterocyclic compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine 2'-deoxyribonucleoside (CHEBI:15698 )
Deoxyribonucleosides (C00881 )

Ontology

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Plant:

Animal

Biological location:

Tissue and substructures:

All tissues

Biofluid and excreta:

Cell and elements:

Extracellular

Subcellular:

Role

Industrial application:

Pharmaceutical industry:

Pharmaceutical

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	207 - 210 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	870 mg/mL	Not Available
logP	-1.77	HANSCH,C ET AL. (1995)

Predicted Properties

Property	Value	Source
logP	-1.9	ALOGPS
logP	-1.9	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	0.31	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	108.38 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	53.03 m³·mol⁻¹	ChemAxon
Polarizability	21.65 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	Deoxycytidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0006-9510000000-43f83823bd8a63669514	Spectrum
Predicted GC-MS	Deoxycytidine, 2 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0gb9-4912000000-fef878d78b0000e850bb	Spectrum
Predicted GC-MS	Deoxycytidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxycytidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxycytidine, TMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxycytidine, TMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxycytidine, TMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxycytidine, TMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxycytidine, TMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxycytidine, TMS_2_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxycytidine, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxycytidine, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxycytidine, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxycytidine, TBDMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxycytidine, TBDMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxycytidine, TBDMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Deoxycytidine, TBDMS_2_4, 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)	splash10-03di-0900000000-27431bdd2327f6f2b886	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-03di-1900000000-0ea85f3f3940843e385b	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-03dl-9500000000-569e473eba0b700f5b6e	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-004i-0090000000-5c8c0fde4f2163fbc335	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-0006-9420000000-28279714b575d59761ce	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-0006-9200000000-df7c76b755c9fac5267b	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0006-9100000000-acbd1d7557be6d716a19	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-00kf-9100000000-056ef35d3aa743e0d5cf	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-03di-0910000000-52e9d173bb94576f7d9e	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-03di-0900000000-e06e5a9f19c4162aa24f	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-03di-0900000000-551d8ee9679ef3fb65fa	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-03di-3900000000-4c62633283ba566dbee0	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive	splash10-03di-0900000000-bac3656523b118a2c1bc	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive	splash10-03dj-6900000000-dfa8435d3dd8b8981621	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positive	splash10-01t9-0690000000-72302b09c51553dde169	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positive	splash10-03fr-0930000000-f5c80400a73719f6211f	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-0006-9130000000-c7f95a478d22e3cc83f4	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-0090000000-af75883dba546c82e7bc	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0006-9420000000-562a675c6278a4ae2bc4	2017-09-14	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-e9d4ffd1148d792f5132	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4900000000-b2a5f419f882d45f6ae7	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-8900000000-0bbcfd7be44c4f38c4fc	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-1890000000-395ff33971fbc8368eca	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0016-4910000000-2dc8aa3aad2b1c83316f	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9200000000-cc82bf3d145faf0a6ca3	2016-09-12	View Spectrum

NMR

Type	Description	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 125 MHz, H₂O, experimental)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, 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
Deoxycytidine kinase	DCK	4q13.3-q21.1	P27707	details
5'(3')-deoxyribonucleotidase, mitochondrial	NT5M		Q9NPB1	details
AID	AID		Q546Y9	details
Cytosolic 5'-nucleotidase 3	NT5C3	7p14.3	Q9H0P0	details
Cytosolic purine 5'-nucleotidase	NT5C2	10q24.32	P49902	details
Cytidine deaminase	CDA	1p36.2-p35	P32320	details
Uridine-cytidine kinase-like 1	UCKL1	20q13.33	Q9NWZ5	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
AID	AID		Q546Y9	details
Cytosolic 5'-nucleotidase 3	NT5C3	7p14.3	Q9H0P0	details
Cytosolic purine 5'-nucleotidase	NT5C2	10q24.32	P49902	details
Cytidine deaminase	CDA	1p36.2-p35	P32320	details
DNA dC->dU-editing enzyme APOBEC-3G	APOBEC3G	22q13.1-q13.2	Q9HC16	details

Receptors

Protein Name	Gene Name	Locus	Uniprot ID	Details
Cytidine deaminase	CDA	1p36.2-p35	P32320	details

Transcriptional Factors

Not Available

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0000014

DrugBank ID

DB02594

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB021871

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

15698

References

General References

Not Available

Only showing the first 10 proteins. There are 22 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. Deoxycytidine kinase

General function:: Involved in ATP binding
Specific function:: Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.
Gene Name:: DCK
Uniprot ID:: P27707
Molecular weight:: 30518.315

Enzyme Details

6. 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

7. AID

General function:: Involved in zinc ion binding
Specific function:: Not Available
Gene Name:: AID
Uniprot ID:: Q546Y9
Molecular weight:: 23953.3

Enzyme Details

8. 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

Enzyme Details

9. Cytosolic purine 5'-nucleotidase

General function:: Involved in 5'-nucleotidase activity
Specific function:: May have a critical role in the maintenance of a constant composition of intracellular purine/pyrimidine nucleotides in cooperation with other nucleotidases. Preferentially hydrolyzes inosine 5'-monophosphate (IMP) and other purine nucleotides.
Gene Name:: NT5C2
Uniprot ID:: P49902
Molecular weight:: 64969.2

Enzyme Details

10. Cytidine deaminase

General function:: Involved in zinc ion binding
Specific function:: This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
Gene Name:: CDA
Uniprot ID:: P32320
Molecular weight:: 16184.545

Only showing the first 10 proteins. There are 22 proteins in total.

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Showing Compound Card for Deoxycytidine (CDB004782)

Structure for CDB004782 (Deoxycytidine)

Enzymes