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dADP (YMDB00901)

Identification
YMDB IDYMDB00901
NamedADP
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptiondADP belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside diphosphates. These are purine nucleotides with diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. dADP is a very strong basic compound (based on its pKa).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 2'-deoxyadenosine-5'-diphosphate
  • dADP
  • deoxyadenosine diphosphate
CAS number2793-06-8
WeightAverage: 411.2017
Monoisotopic: 411.034500127
InChI KeyDAEAPNUQQAICNR-GFCOJPQKSA-N
InChIInChI=1S/C10H15N5O9P2/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(23-7)2-22-26(20,21)24-25(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7?/m0/s1
IUPAC Name[({[(2R,3S)-5-(6-amino-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional IUPAC Name{[(2R,3S)-5-(6-aminopurin-9-yl)-3-hydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid
Chemical FormulaC10H15N5O9P2
SMILES[H]O[C@@]1([H])C([H])([H])C([H])(O[C@]1([H])C([H])([H])OP(=O)(O[H])OP(=O)(O[H])O[H])N1C([H])=NC2=C1N=C([H])N=C2N([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside diphosphates. These are purine nucleotides with diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine deoxyribonucleotides
Direct ParentPurine 2'-deoxyribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine 2'-deoxyribonucleoside diphosphate
  • 6-aminopurine
  • Organic pyrophosphate
  • Imidazopyrimidine
  • Purine
  • Aminopyrimidine
  • Monoalkyl phosphate
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Imidolactam
  • Heteroaromatic compound
  • Azole
  • Tetrahydrofuran
  • Imidazole
  • Secondary alcohol
  • Azacycle
  • Organoheterocyclic compound
  • Oxacycle
  • Organic oxygen compound
  • Organic oxide
  • Alcohol
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Amine
  • Primary amine
  • Hydrocarbon derivative
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility2.8 g/LALOGPS
logP-1.6ALOGPS
logP-4.4ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
pKa (Strongest Basic)5.01ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area212.37 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity83.43 m³·mol⁻¹ChemAxon
Polarizability33.53 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • nucleus
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
purine nucleotides de novo biosynthesisPW002478 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Purine metabolismec00230 Map00230
SMPDB Reactions
dADP + Adenosine triphosphate → ADP + dATP
ADP + reduced thioredoxin ↔ water + oxidized thioredoxin + dADP
ADP + a reduced NrdH glutaredoxin-like protein → an oxidized NrdH glutaredoxin-like protein + water + dADP
KEGG Reactions
Adenosine triphosphate + dAMP ↔ dADP + ADP
Guanosine monophosphate + dATP ↔ dADP + Guanosine diphosphate
Adenosine triphosphate + dADP ↔ dATP + ADP
thioredoxin dithiol + ADP → dADP + thioredoxin disulfide + water
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-002g-6912000000-79e00145ccc9b13e6929JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-004m-6911200000-e5bf41ca8aa765fc86eaJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0901000000-8ca1882bf2be011f491eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-85ff133b10a7cade586cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-0900000000-61ac8ef338ec6bb84314JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0602900000-ae11f56ebe4579143453JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0560-4900000000-672539848df9fba4f8bfJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-2485964b0c6e0be9f916JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Bao, J., Ryu, D. D. (2006). "Cloning of deoxynucleoside monophosphate kinase genes and biosynthesis of deoxynucleoside diphosphates." Biotechnol Bioeng 93:572-580.16240436
  • Guetsova, M. L., Lecoq, K., Daignan-Fornier, B. (1997). "The isolation and characterization of Saccharomyces cerevisiae mutants that constitutively express purine biosynthetic genes." Genetics 147:383-397.9335580
Synthesis Reference:Nara, Takashi; Misawa, Masanaru. Bacterial phosphorylation of 5'-deoxyadenosine monophosphate to di- or triphosphate. Jpn. Tokkyo Koho (1971), 2 pp.
External Links:
ResourceLink
CHEBI ID16174
HMDB IDHMDB01508
Pubchem Compound ID188966
Kegg IDC00206
ChemSpider ID24785085
FOODB IDFDB022662
WikipediaDeoxyadenosine_diphosphate
BioCyc IDDADP

Enzymes

Protein Details
1. Ribonucleoside-diphosphate reductase small chain 1
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR2 provides the diiron-tyrosyl radical center
Gene Name:
RNR2
Uniprot ID:
P09938
Molecular weight:
46147.0
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.
Protein Details
2. Nucleoside diphosphate kinase
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. Required for repair of UV radiation- and etoposide-induced DNA damage
Gene Name:
YNK1
Uniprot ID:
P36010
Molecular weight:
17166.59961
Reactions
ATP + nucleoside diphosphate → ADP + nucleoside triphosphate.
Protein Details
3. Ribonucleoside-diphosphate reductase large chain 1
General function:
Involved in oxidation-reduction process
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
Gene Name:
RNR1
Uniprot ID:
P21524
Molecular weight:
99560.20313
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.
Protein Details
4. Guanylate kinase
General function:
Involved in protein binding
Specific function:
Essential for recycling GMP and indirectly, cGMP
Gene Name:
GUK1
Uniprot ID:
P15454
Molecular weight:
20637.19922
Reactions
ATP + GMP → ADP + GDP.
Protein Details
5. Ribonucleoside-diphosphate reductase large chain 2
General function:
Involved in oxidation-reduction process
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
Gene Name:
RNR3
Uniprot ID:
P21672
Molecular weight:
97513.79688
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.