Adenosine 3',5'-diphosphate (PAMDB000022)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000022
Identification
Name: Adenosine 3',5'-diphosphate
Description:Adenosine 3', 5'-diphosphate or PAP is a nucleotide that is closely related to ADP. It has two phosphate groups attached to the 5' and 3' positions of the pentose sugar ribose (instead of pyrophosphoric acid at the 5' position, as found in ADP), and the nucleobase adenine. PAP is converted to 3'-phosphoadenosine 5'-phosphosulfate (PAPS) by Sulfotransferase and then back to PAP after the sulfotransferase reaction. Sulfotransferase (STs) catalyze the transfer reaction of the sulfate group from the ubiquitous donor 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to an acceptor group of numerous substrates. This reaction, often referred to as sulfuryl transfer, sulfation, or sulfonation plays a key role in various biological processes such as cell communication, growth and development, and defense. (HMDB) PAP is involved in sulfur metabolism in Pseudomonas aeruginosa, and can be converted into AMP and subsequently ADP by enzymes. (PMID 10939241)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 3',5'-ADP
  • 3'-Phosphoryl-AMP
  • 3,5-ADP
  • 3,5-Diphosphoadenosine
  • 3-Phosphoadenosine 5-phosphate
  • 3-Phosphoadenosine 5-phosphoric acid
  • 5-(Dihydrogen phosphate) 3-Adenylate
  • 5-(Dihydrogen phosphate) 3-Adenylic acid
  • 5-(Dihydrogen phosphate)3'-Adenylate
  • 5-(Dihydrogen phosphate)3'-Adenylic acid
  • 5-(Dihydrogen phosphoric acid) 3-adenylic acid
  • 5-(Dihydrogen phosphoric acid)3'-adenylic acid
  • Adenosine 3',5'-bisphosphate
  • Adenosine 3',5'-bisphosphoric acid
  • Adenosine 3',5'-diphosphoric acid
  • Adenosine 3,5-bis
  • Adenosine 3,5-bisphosphate
  • Adenosine 3,5-bisphosphoric acid
  • Adenosine 3,5-diphosphate
  • Adenosine 3,5-diphosphoric acid
  • Adenosine-3',5'-bisphosphate
  • Adenosine-3',5'-bisphosphoric acid
  • PAP
  • Phosphoadenosine phosphate
  • Phosphoadenosine phosphoric acid
Chemical Formula: C10H15N5O10P2
Average Molecular Weight: 427.2011
Monoisotopic Molecular Weight: 427.029414749
InChI Key: WHTCPDAXWFLDIH-KQYNXXCUSA-N
InChI:InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(25-27(20,21)22)4(24-10)1-23-26(17,18)19/h2-4,6-7,10,16H,1H2,(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/t4-,6-,7-,10-/m1/s1
CAS number: 1053-73-2
IUPAC Name:{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Name: adenosine 3',5'-bisphosphate
SMILES:NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(O)(O)=O)[C@@H](OP(O)(O)=O)[C@H]1O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as purine ribonucleoside 3',5'-bisphosphates. These are purine ribobucleotides with one phosphate group attached to 3' and 5' hydroxyl groups of the ribose moiety.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Purine nucleotides
Sub ClassPurine ribonucleotides
Direct Parent Purine ribonucleoside 3',5'-bisphosphates
Alternative Parents
Substituents
  • Purine ribonucleoside 3',5'-bisphosphate
  • Purine ribonucleoside monophosphate
  • N-glycosyl compound
  • Glycosyl compound
  • Monosaccharide phosphate
  • 6-aminopurine
  • Purine
  • Imidazopyrimidine
  • Monoalkyl phosphate
  • Aminopyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Pyrimidine
  • Primary aromatic amine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • N-substituted imidazole
  • Monosaccharide
  • Saccharide
  • Heteroaromatic compound
  • Oxolane
  • Imidazole
  • Azole
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular Framework Aromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-4
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Water Solubility:614.5 mg/mL [HMP experimental]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility3.33 mg/mLALOGPS
logP-1.6ALOGPS
logP-6.1ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)0.71ChemAxon
pKa (Strongest Basic)4.92ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area232.6 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity84.94 m3·mol-1ChemAxon
Polarizability34.31 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
glutaredoxin + Phosphoadenosine phosphosulfate > glutaredoxin +2 Hydrogen ion + Adenosine 3',5'-diphosphate + Sulfite
Phosphoadenosine phosphosulfate + Reduced Thioredoxin >2 Hydrogen ion + Adenosine 3',5'-diphosphate + Sulfite + Oxidized Thioredoxin
apoprotein [acyl carrier protein] + Coenzyme A > acyl carrier protein + Hydrogen ion + Adenosine 3',5'-diphosphate
Water + Adenosine 3',5'-diphosphate > Adenosine monophosphate + Phosphate
Coenzyme A + Apo-[acyl-carrier-protein] <> Adenosine 3',5'-diphosphate + Acyl-carrier protein + Acyl-carrier protein
Thioredoxin + Phosphoadenosine phosphosulfate + Thioredoxin disulfide <> Thioredoxin disulfide + Sulfite + Adenosine 3',5'-diphosphate + Thioredoxin
CoA-(4'-phosphopantetheine) + apo-[acyl-carrier-protein] > Adenosine 3',5'-diphosphate + holo-[acyl-carrier-protein]
Adenosine 3',5'-diphosphate + Sulfite + thioredoxin disulfide > Phosphoadenosine phosphosulfate + thioredoxin
Adenosine 3',5'-diphosphate + Water > Adenosine monophosphate + Inorganic phosphate
Phosphoadenosine phosphosulfate + reduced thioredoxin > Sulfite +2 Hydrogen ion + Adenosine 3',5'-diphosphate +2 oxidized thioredoxin + Sulfite + Adenosine 3',5'-diphosphate
Phosphoadenosine phosphosulfate + reduced thioredoxin > Sulfite + oxidized thioredoxin + Hydrogen ion + Adenosine 3',5'-diphosphate + Sulfite + Adenosine 3',5'-diphosphate
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0902300000-77268ef9fe8672f81e9fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0900000000-6986eb10675f363acf42View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-1900000000-493254661a51349997bdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-7801900000-b4b0af4deca129a6a12cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0059-9800000000-4a1ffcf05d9938fe121eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9200000000-fb4a5bf16d0e5bcaa1e0View in MoNA
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Gasmi L, McLennan AG: The mouse Nudt7 gene encodes a peroxisomal nudix hydrolase specific for coenzyme A and its derivatives. Biochem J. 2001 Jul 1;357(Pt 1):33-8. Pubmed: 11415433
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • 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
  • Leonidas DD, Chavali GB, Oikonomakos NG, Chrysina ED, Kosmopoulou MN, Vlassi M, Frankling C, Acharya KR: High-resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure-based design of ribonucleolytic inhibitors. Protein Sci. 2003 Nov;12(11):2559-74. Pubmed: 14573867
  • Lewis AJ, Otake Y, Walle UK, Walle T: Sulphonation of N-hydroxy-2-acetylaminofluorene by human dehydroepiandrosterone sulphotransferase. Xenobiotica. 2000 Mar;30(3):253-61. Pubmed: 10752640
  • Russo N, Acharya KR, Vallee BL, Shapiro R: A combined kinetic and modeling study of the catalytic center subsites of human angiogenin. Proc Natl Acad Sci U S A. 1996 Jan 23;93(2):804-8. Pubmed: 8570639
  • Sekowska, A., Kung, H. F., Danchin, A. (2000). "Sulfur metabolism in Escherichia coli and related bacteria: facts and fiction." J Mol Microbiol Biotechnol 2:145-177. Pubmed: 10939241
  • Traut TW: Physiological concentrations of purines and pyrimidines. Mol Cell Biochem. 1994 Nov 9;140(1):1-22. Pubmed: 7877593
  • Turner NA, Moake JL, McIntire LV: Blockade of adenosine diphosphate receptors P2Y(12) and P2Y(1) is required to inhibit platelet aggregation in whole blood under flow. Blood. 2001 Dec 1;98(12):3340-5. Pubmed: 11719372
Synthesis Reference: Tsunako, Mitsutomo; Kotone, Akira. Preparation of nucleoside-2',5'- and 3',5'-diphosphoric acids. Jpn. Kokai Tokkyo Koho (1991), 13 pp.
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID17985
HMDB IDHMDB00061
Pubchem Compound ID159296
Kegg IDC00054
ChemSpider ID140102
Wikipedia IDNot Available
BioCyc ID3-5-ADP
EcoCyc ID3-5-ADP
Ligand ExpoA3P

Enzymes

Protein Details
• Phosphoadenosine phosphosulfate reductase
General function:
Involved in phosphoadenylyl-sulfate reductase (thioredoxin) activity
Specific function:
Reduction of activated sulfate into sulfite
Gene Name:
cysH
Locus Tag:
PA1756
Molecular weight:
30.2 kDa
Reactions
Adenosine 3',5'-bisphosphate + sulfite + thioredoxin disulfide = 3'-phosphoadenylyl sulfate + thioredoxin.
Protein Details
• 3'(2'),5'-bisphosphate nucleotidase cysQ
General function:
Involved in magnesium ion binding
Specific function:
Converts 3'(2')-phosphoadenosine 5'-phosphate (PAP) to AMP. May also convert adenosine 3'-phosphate 5'-phosphosulfate (PAPS) to adenosine 5'-phosphosulfate (APS). Has 10000-fold lower activity towards inositol 1,4-bisphosphate (Ins(1,4)P2)
Gene Name:
cysQ
Locus Tag:
PA5175
Molecular weight:
29.8 kDa
Reactions
Adenosine 3',5'-bisphosphate + H(2)O = adenosine 5'-phosphate + phosphate.
Protein Details
• Glutaredoxin-4
General function:
Involved in electron carrier activity
Specific function:
Monothiol glutaredoxin involved in the biogenesis of iron-sulfur clusters (Probable)
Gene Name:
grxD
Locus Tag:
PA3533
Molecular weight:
11.8 kDa
Protein Details
• Glutaredoxin-3
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
Locus Tag:
PA5129
Molecular weight:
9.2 kDa
Protein Details
• Thioredoxin-1
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
Locus Tag:
PA5240
Molecular weight:
11.9 kDa