Record Information
Version2.0
Creation Date2012-07-30 14:55:18 -0600
Update Date2015-09-17 15:41:12 -0600
Secondary Accession Numbers
  • ECMDB21326
Identification
Name:dADP
Description:Deoxyadenosine diphosphate is a nucleoside diphosphate. It is related to the common nucleic acid ATP, or adenosine triphosphate, with the -OH (hydroxyl) group on the 2' carbon on the nucleotide's pentose removed (hence the deoxy- part of the name), and with one fewer phosphoryl group than ATP.
Structure
Thumb
Synonyms:
  • 2'-Deoxyadenosine 5'-(trihydrogen diphosphate)
  • 2'-Deoxyadenosine 5'-(trihydrogen diphosphoric acid)
  • 2'-Deoxyadenosine 5'-diphosphate
  • 2'-Deoxyadenosine 5'-diphosphoric acid
  • 2'-Deoxyadenosine-5'-diphosphate
  • 2'-Deoxyadenosine-5'-diphosphoric acid
  • 2-Deoxyadenosine 5-diphosphate
  • 2-Deoxyadenosine 5-diphosphoric acid
  • DADP
  • Deoxyadenosine diphosphate
  • Deoxyadenosine diphosphoric acid
  • Deoxyadenosine-diphosphate
  • Deoxyadenosine-diphosphoric acid
Chemical Formula:C10H15N5O9P2
Weight:Average: 411.2017
Monoisotopic: 411.034500127
InChI Key:DAEAPNUQQAICNR-GFCOJPQKSA-N
InChI:InChI=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
CAS number:Not Available
IUPAC Name:[({[(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional IUPAC Name:dADP
SMILES:NC1=NC=NC2=C1N=CN2C1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities 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.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub ClassPurine nucleotides
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
  • Primary aromatic amine
  • Pyrimidine
  • Alkyl phosphate
  • Imidolactam
  • Heteroaromatic compound
  • Imidazole
  • Azole
  • Tetrahydrofuran
  • Secondary alcohol
  • Azacycle
  • Organoheterocyclic compound
  • Oxacycle
  • Hydrocarbon derivative
  • Organic oxide
  • Alcohol
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Amine
  • Primary amine
  • Organic oxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility2.8 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity83.43 m3·mol-1ChemAxon
Polarizability33.6 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
purine nucleotides de novo biosynthesisPW000910 Pw000910Pw000910 greyscalePw000910 simple
purine nucleotides de novo biosynthesis 1435709748PW000960 Pw000960Pw000960 greyscalePw000960 simple
purine nucleotides de novo biosynthesis 2PW002033 Pw002033Pw002033 greyscalePw002033 simple
KEGG Pathways:Not Available
EcoCyc Pathways:
  • adenosine nucleotides de novo biosynthesis PWY-6126
Concentrations
ConcentrationStrainMediaGrowth StatusGrowth SystemTemperatureDetails
53± 0 uMBW2511348 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 45 mM (NH4)2SO4, supplemented with 1 mM MgSO4, 1 mg/l thiamine·HCl, 5.6 mg/l CaCl2, 8 mg/l FeCl3, 1 mg/l MnCl2·4H2O, 1.7 mg/l ZnCl2, 0.43 mg/l CuCl2·2H2O, 0.6 mg/l CoCl2·2H2O and 0.6 mg/l Na2MoO4·2H2O. 4 g/L GlucoStationary Phase, glucose limitedBioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h37 oCPMID: 17379776
Find out more about how we convert literature concentrations.
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0901000000-81bcc9c0732abcab5587View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-07e1d9f74d49eff2efacView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-0900000000-fbafa2b04b5f162aeaccView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0602900000-f99abf5b772cd38d9906View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0059-6900000000-e7f368f6a5bcd9cdbdb9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-9e49ebc21922de6f1976View in MoNA
References
References:
  • Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. Pubmed: 17379776
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID16174
HMDB IDHMDB01508
Pubchem Compound ID188966
Kegg IDC00206
ChemSpider ID164196
WikipediaDADP
BioCyc IDDADP
EcoCyc IDDADP
Ligand ExpoDAT

Enzymes

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. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox- active cysteines
Gene Name:
nrdA
Uniprot ID:
P00452
Molecular weight:
85774
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
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:
ndk
Uniprot ID:
P0A763
Molecular weight:
15463
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
General function:
Involved in ATP binding
Specific function:
ATP + uridine = ADP + UMP
Gene Name:
udk
Uniprot ID:
P0A8F4
Molecular weight:
24353
Reactions
ATP + uridine = ADP + UMP.
ATP + cytidine = ADP + CMP.
General function:
Involved in magnesium ion binding
Specific function:
ATP + pyruvate = ADP + phosphoenolpyruvate
Gene Name:
pykF
Uniprot ID:
P0AD61
Molecular weight:
50729
Reactions
ATP + pyruvate = ADP + phosphoenolpyruvate.
General function:
Involved in electron carrier activity
Specific function:
Efficient electron donor for the essential enzyme ribonucleotide reductase. Is also able to reduce the interchain disulfide bridges of insulin
Gene Name:
trxC
Uniprot ID:
P0AGG4
Molecular weight:
15555
Reactions
Protein dithiol + NAD(P)(+) = protein disulfide + NAD(P)H.
General function:
Involved in magnesium ion binding
Specific function:
ATP + pyruvate = ADP + phosphoenolpyruvate
Gene Name:
pykA
Uniprot ID:
P21599
Molecular weight:
51357
Reactions
ATP + pyruvate = ADP + phosphoenolpyruvate.
General function:
Involved in catalytic activity
Specific function:
2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H(2)O = ribonucleoside triphosphate + thioredoxin
Gene Name:
nrdD
Uniprot ID:
P28903
Molecular weight:
80022
Reactions
2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H(2)O = ribonucleoside triphosphate + thioredoxin.
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2F contains the tyrosyl radical required for catalysis
Gene Name:
nrdF
Uniprot ID:
P37146
Molecular weight:
36443
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
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. R1E contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide
Gene Name:
nrdE
Uniprot ID:
P39452
Molecular weight:
80478
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
General function:
Involved in ATP binding
Specific function:
Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth
Gene Name:
adk
Uniprot ID:
P69441
Molecular weight:
23586
Reactions
ATP + AMP = 2 ADP.
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis
Gene Name:
nrdB
Uniprot ID:
P69924
Molecular weight:
43517
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
General function:
Involved in electron carrier activity
Specific function:
Monothiol glutaredoxin involved in the biogenesis of iron-sulfur clusters (Probable)
Gene Name:
grxD
Uniprot ID:
P0AC69
Molecular weight:
12879
General function:
Involved in electron carrier activity
Specific function:
The disulfide bond functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. In addition, it is also involved in reducing some disulfides in a coupled system with glutathione reductase
Gene Name:
grxC
Uniprot ID:
P0AC62
Molecular weight:
9137
General function:
Involved in protein binding
Specific function:
Involved in reducing some disulfides in a coupled system with glutathione reductase. Does not act as hydrogen donor for ribonucleotide reductase
Gene Name:
grxB
Uniprot ID:
P0AC59
Molecular weight:
24350
General function:
Involved in electron carrier activity
Specific function:
The disulfide bond functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. In addition, it is also involved in reducing some disulfides in a coupled system with glutathione reductase
Gene Name:
grxA
Uniprot ID:
P68688
Molecular weight:
9685
General function:
Involved in electron carrier activity
Specific function:
Participates in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyzes dithiol-disulfide exchange reactions
Gene Name:
trxA
Uniprot ID:
P0AA25
Molecular weight:
11807

Transporters

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:
ndk
Uniprot ID:
P0A763
Molecular weight:
15463
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.