Showing metabocard for dGDP (BMDB0000960)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (4) Show 4 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:39:10 UTC
Update Date2020-05-21 16:28:54 UTC
BMDB IDBMDB0000960
Secondary Accession Numbers
  • BMDB00960
Metabolite Identification
Common NamedGDP
DescriptiondGDP, 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
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
2'-Deoxyguanosine 5'-diphosphateChEBI
Deoxyguanosine diphosphateChEBI
2'-Deoxyguanosine 5'-diphosphoric acidGenerator
Deoxyguanosine diphosphoric acidGenerator
2'-Deoxy-GDPHMDB
2'-Deoxyguanosine-5'-diphosphateHMDB
5'-dGDPHMDB
Deoxyguanosine 5'-diphosphateHMDB
Deoxyguanosine-diphosphateHMDB
Chemical FormulaC10H15N5O10P2
Average Molecular Weight427.2011
Monoisotopic Molecular Weight427.029414749
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 NamedGDP
CAS Registry Number3493-09-2
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 KeyCIKGWCTVFSRMJU-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.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassCinnamic acids and derivatives
Sub ClassHydroxycinnamic acids and derivatives
Direct ParentHydroxycinnamic 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 FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility5.5 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.4ALOGPS
logP-2.5ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)1.79ChemAxon
pKa (Strongest Basic)0.44ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area228.05 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity84.86 m³·mol⁻¹ChemAxon
Polarizability34.99 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0000960
DrugBank IDDB03491
Phenol Explorer Compound IDNot Available
FooDB IDFDB022338
KNApSAcK IDC00019355
Chemspider ID388359
KEGG Compound IDC00361
BioCyc IDDGDP
BiGG ID34741
Wikipedia LinkDeoxyguanosine_diphosphate
METLIN ID5906
PubChem Compound439220
PDB IDNot Available
ChEBI ID28862
References
Synthesis ReferenceKlenow, Hans; Lichtler, Eleanor; Andersen, Bjorn. Adenine deoxyriboside polyphosphates. Acta Chemica Scandinavica (1956), 10 159-60
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot 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 + dGTPdetails
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 + dGDPdetails
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 + Thioredoxindetails
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 + Thioredoxindetails