Cannabis Compound Database: Showing Compound Card for dGDP (CDB004874)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (16) Show 27 proteins XML

Record Information

Version

1.0

Created at

2020-04-17 18:45:43 UTC

Updated at

2020-11-18 16:38:54 UTC

CannabisDB ID

CDB004874

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

dGDP

Description

dGDP, also known as 2'-deoxy-GDP or 5'-dGDP, belongs to the class of organic compounds known as hydroxycinnamic acids. Hydroxycinnamic acids are compounds containing an cinnamic acid where the benzene ring is hydroxylated. dGDP is a moderately basic compound (based on its pKa). dGDP exists in all eukaryotes, ranging from yeast to humans. Within humans, dGDP participates in a number of enzymatic reactions. In particular, dGDP can be converted into dGTP; which is mediated by the enzyme nucleoside diphosphate kinase 6. In addition, dGDP can be biosynthesized from 2'-deoxyguanosine 5'-monophosphate through its interaction with the enzyme guanylate kinase. In humans, dGDP is involved in the metabolic disorder called the gout or kelley-seegmiller syndrome pathway. Outside of the human body, dGDP has been detected, but not quantified in, several different foods, such as chinese bayberries, thistles, french plantains, nopals, and pepper (capsicum). This could make dGDP a potential biomarker for the consumption of these foods. A purine 2'-deoxyribonucleoside 5'-diphosphate having guanine as the nucleobase. dGDP 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'-Deoxyguanosine 5'-diphosphate	ChEBI
Deoxyguanosine diphosphate	ChEBI
2'-Deoxyguanosine 5'-diphosphoric acid	Generator
Deoxyguanosine diphosphoric acid	Generator
2'-Deoxy-GDP	HMDB
2'-Deoxyguanosine-5'-diphosphate	HMDB
5'-dGDP	HMDB
Deoxyguanosine 5'-diphosphate	HMDB
Deoxyguanosine-diphosphate	HMDB

Chemical Formula

C₁₀H₁₅N₅O₁₀P₂

Average Molecular Weight

427.2

Monoisotopic Molecular Weight

427.0294

IUPAC Name

[({[(2R,3S,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional Name

dGDP

CAS Registry Number

3493-09-2

SMILES

NC1=NC2=C(N=CN2[C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O2)C(=O)N1

InChI Identifier

InChI=1S/C10H15N5O10P2/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1

InChI Key

CIKGWCTVFSRMJU-KVQBGUIXSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxycinnamic acids. Hydroxycinnamic acids are compounds containing an cinnamic acid where the benzene ring is hydroxylated.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Cinnamic acids and derivatives

Sub Class

Hydroxycinnamic acids and derivatives

Direct Parent

Hydroxycinnamic acids

Alternative Parents

Substituents

Cinnamic acid
Coumaric acid or derivatives
Hydroxycinnamic acid
Methoxyphenol
Phenoxy compound
Anisole
Methoxybenzene
Styrene
Phenol ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Monocyclic benzene moiety
Benzenoid
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Ether
Organic oxygen compound
Carbonyl group
Organic oxide
Organooxygen compound
Hydrocarbon derivative
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

ferulic acids (CHEBI:27794 )

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	5.5 mg/mL	Not Available
logP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1.4	ALOGPS
logP	-2.5	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	1.79	ChemAxon
pKa (Strongest Basic)	0.44	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	228.05 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	84.86 m³·mol⁻¹	ChemAxon
Polarizability	34.99 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
Predicted GC-MS	dGDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-056v-8931100000-80ef9c9f635e7c791ca3	Spectrum
Predicted GC-MS	dGDP, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-006w-9273200000-8578b4069f91a1e37a93	Spectrum
Predicted GC-MS	dGDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	dGDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	dGDP, TMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	dGDP, TMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	dGDP, TMS_1_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	dGDP, TMS_1_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	dGDP, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	dGDP, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	dGDP, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	dGDP, TBDMS_1_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	dGDP, TBDMS_1_5, 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	splash10-004i-9600800000-36eca5667f3968858676	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - , positive	splash10-0udi-2910000000-7d78949fd021bc9a3e84	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-056r-5921800000-485a79c4e3311f328cf1	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9200000000-6e2fd4ae48d17fdbe9ae	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0000900000-f578c8db6d6baa91f146	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-0udi-1900000000-eada75fb37d52199dc57	2021-09-20	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0901100000-8f9213d3d0d12989aa4e	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900000000-fe32d673485e026f7ffd	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-0900000000-f9d9c2d10a52b1295c20	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0500900000-f643b08ebfbee486ac88	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-056r-4900000000-614b7240ac447b1cf302	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-ebc82fc4fdc1243cf001	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0000900000-2f685e4ebf6e3f21813b	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9221200000-d3ab4261ce93db5c0d8f	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0900100000-b27de50984aa34aec15e	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900000000-361a2474138028086bb3	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-0921000000-ed51ef3ce7f119c2cbc3	2021-09-22	View Spectrum

NMR

Not Available

Pathways

Name	SMPDB/Pathwhiz	KEGG
Purine Metabolism
Adenosine Deaminase Deficiency		Not Available
Adenylosuccinate Lyase Deficiency		Not Available
Gout or Kelley-Seegmiller Syndrome		Not Available
Lesch-Nyhan Syndrome (LNS)		Not Available

Protein Targets

Enzymes

Protein Name	Gene Name	Locus	Uniprot ID	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
Pyruvate kinase isozymes M1/M2	PKM	15q22	P14618	details
Pyruvate kinase isozymes R/L	PKLR	1q21	P30613	details
Guanylate kinase	GUK1	1q32-q41	Q16774	details
Uridine-cytidine kinase 2	UCK2	1q23	Q9BZX2	details
Ribonucleoside-diphosphate reductase subunit M2 B	RRM2B	8q23.1	Q7LG56	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
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

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

HMDB0000960

DrugBank ID

DB03491

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Deoxyguanosine_diphosphate

METLIN ID

5906

PubChem Compound

439220

PDB ID

Not Available

ChEBI ID

28862

References

General References

Not Available

Only showing the first 10 proteins. There are 27 proteins in total.

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Enzymes

Enzyme Details

1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

Enzyme Details

10. Pyruvate kinase isozymes M1/M2

General function:: Involved in magnesium ion binding
Specific function:: Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation. Plays a general role in caspase independent cell death of tumor cells. The ratio betwween the highly active tetrameric form and nearly inactive dimeric form determines whether glucose carbons are channeled to biosynthetic processes or used for glycolytic ATP production. The transition between the 2 forms contributes to the control of glycolysis and is important for tumor cell proliferation and survival.
Gene Name:: PKM
Uniprot ID:: P14618
Molecular weight:: 65930.14

Only showing the first 10 proteins. There are 27 proteins in total.

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Showing Compound Card for dGDP (CDB004874)

Structure for CDB004874 (dGDP)

Enzymes