Bovine Metabolome Database: Showing metabocard for dGDP (BMDB0000960)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (4) Show 4 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:39:10 UTC

Update Date

2020-05-21 16:28:54 UTC

BMDB ID

BMDB0000960

Secondary Accession Numbers

BMDB00960

Metabolite 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.

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

427.2011

Monoisotopic Molecular Weight

427.029414749

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

Status

Expected but not Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cytoplasm
Mitochondria
Nucleus

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	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-056v-8931100000-80ef9c9f635e7c791ca3	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-006w-9273200000-8578b4069f91a1e37a93	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_5) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-004i-9600800000-36eca5667f3968858676	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - , positive	splash10-0udi-2910000000-7d78949fd021bc9a3e84	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-056r-5921800000-485a79c4e3311f328cf1	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9200000000-6e2fd4ae48d17fdbe9ae	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0000900000-f578c8db6d6baa91f146	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-0udi-1900000000-eada75fb37d52199dc57	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0901100000-8f9213d3d0d12989aa4e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900000000-fe32d673485e026f7ffd	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-0900000000-f9d9c2d10a52b1295c20	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0500900000-f643b08ebfbee486ac88	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-056r-4900000000-614b7240ac447b1cf302	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-ebc82fc4fdc1243cf001	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0000900000-2f685e4ebf6e3f21813b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9221200000-d3ab4261ce93db5c0d8f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0900100000-b27de50984aa34aec15e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900000000-361a2474138028086bb3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-0921000000-ed51ef3ce7f119c2cbc3	View in MoNA
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cytoplasm
Mitochondria
Nucleus

Biospecimen Locations

Not Available

Pathways

Name	SMPDB/Pathwhiz	KEGG
Purine Metabolism		Not Available

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0000960

DrugBank ID

DB03491

Phenol Explorer Compound ID

Not Available

FooDB 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

Synthesis Reference

Klenow, Hans; Lichtler, Eleanor; Andersen, Bjorn. Adenine deoxyriboside polyphosphates. Acta Chemica Scandinavica (1956), 10 159-60

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. Nucleoside diphosphate kinase 7

General function:: Nucleotide transport and metabolism
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 (By similarity).
Gene Name:: NME7
Uniprot ID:: Q5E9Y9
Molecular weight:: 42599.0

Reactions

Adenosine triphosphate + dGDP → ADP + dGTP	details

Enzyme Details

2. Guanylate kinase

General function:: Nucleotide transport and metabolism
Specific function:: Catalyzes the phosphorylation of GMP to GDP. Essential enzyme for recycling GMP and indirectly, cyclic GMP (cGMP) (PubMed:8243671, PubMed:29515371, PubMed:7911663). Involved in the cGMP metabolism in photoreceptors (PubMed:29515371, PubMed:8243671).
Gene Name:: GUK1
Uniprot ID:: P46195
Molecular weight:: 21910.0

Reactions

Adenosine triphosphate + 2'-Deoxyguanosine 5'-monophosphate → ADP + dGDP	details

Enzyme Details

3. Ribonucleotide reductase regulatory subunit M2

General function:: Not Available
Specific function:: Not Available
Gene Name:: RRM2
Uniprot ID:: E1BI58
Molecular weight:: 44821.0

Reactions

dGDP + Thioredoxin Disulfide + Water → Guanosine diphosphate + Thioredoxin	details

Enzyme Details

4. Ribonucleoside-diphosphate reductase

General function:: Not Available
Specific function:: Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.
Gene Name:: RRM1
Uniprot ID:: F1MSF1
Molecular weight:: 89991.0

Reactions

dGDP + Thioredoxin Disulfide + Water → Guanosine diphosphate + Thioredoxin	details

Showing metabocard for dGDP (BMDB0000960)

Structure for BMDB0000960 (dGDP)

Enzymes

Reactions

Reactions

Reactions

Reactions