ADP-D-ribose (YMDB00967)

Identification

YMDB ID

YMDB00967

Name

ADP-D-ribose

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

ADP-D-ribose, also known as ADP-rib or (rib5)ppa, belongs to the class of organic compounds known as purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group. ADP-D-ribose is a strong basic compound (based on its pKa). ADP-D-ribose exists in both E. coli (prokaryote) and yeast (eukaryote).

Structure

MOL SDF PDB SMILES InChI

Synonyms

(Rib5)ppA
5-(adenosine 5'-pyrophosphoryl)-D-ribose
A5'pp5Rib
adenine-diphosphate-ribose
adenosine 5'-(trihydrogen diphosphate), P'-5-ester with D-ribose
adenosine 5'-diphosphoribose
adenosine 5'-pyrophosphate, 5'-5-ester with D-ribofuranose
adenosine diphosphate ribose
AdoPPRib
ADP ribose
ADP-Rib
adp-ribose
ADP-riboses
ADPribose
D-ribofuranose, 5-5'-ester with adenosine 5'-(trihydrogen pyrophosphate)
ribose adenosinediphosphate
Adenosine 5'-(trihydrogen diphosphoric acid), p'-5-ester with D-ribose
Adenosine 5'-pyrophosphoric acid, 5'-5-ester with D-ribofuranose
Adenosine diphosphoric acid ribose
D-Ribofuranose, 5-5'-ester with adenosine 5'-(trihydrogen pyrophosphoric acid)
Ribose adenosinediphosphoric acid

CAS number

Not Available

Weight

Average: 559.3157
Monoisotopic: 559.071673493

InChI Key

SRNWOUGRCWSEMX-TYASJMOZSA-N

InChI

InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15?/m1/s1

IUPAC Name

{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[hydroxy({[(2R,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methoxy})phosphoryl]oxy})phosphinic acid

Traditional IUPAC Name

adp-D-ribose

Chemical Formula

C₁₅H₂₃N₅O₁₄P₂

SMILES

NC1=C2N=CN([C@@H]3O[C@H](COP(O)(=O)OP(O)(=O)OC[C@H]4OC(O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O)C2=NC=N1

Chemical Taxonomy

Description

belongs to the class of organic compounds known as purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine nucleotide sugars

Direct Parent

Purine nucleotide sugars

Alternative Parents

Substituents

Purine nucleotide sugar
Purine ribonucleoside diphosphate
Purine ribonucleoside monophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
6-aminopurine
Monosaccharide phosphate
Organic pyrophosphate
Imidazopyrimidine
Purine
Aminopyrimidine
Monoalkyl phosphate
Pyrimidine
Alkyl phosphate
Imidolactam
Phosphoric acid ester
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Tetrahydrofuran
Azole
Imidazole
Heteroaromatic compound
Secondary alcohol
Hemiacetal
Organoheterocyclic compound
Polyol
Azacycle
Oxacycle
Organic oxide
Amine
Alcohol
Organopnictogen compound
Organic oxygen compound
Primary amine
Hydrocarbon derivative
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

ADP-sugar (CHEBI:16960 )

Physical Properties

State

Solid

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	3.61 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-6.7	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	1.86	ChemAxon
pKa (Strongest Basic)	5	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	291.52 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	111.12 m³·mol⁻¹	ChemAxon
Polarizability	47.14 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

Not Available

Organoleptic Properties

Not Available

SMPDB Pathways

Not Available

KEGG Pathways

Purine metabolism

ec00230

SMPDB Reactions

Not Available

KEGG Reactions

Not Available

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0910130000-b9073b1bbcee0d4c7c6e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0910000000-4407a7719b31b18bb57b	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-1900000000-9d6c2b567f9da9d1d1ce	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a59-1701390000-e958d4521e35989750e1	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-1910100000-a653cbe7cba6b5fab234	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a7i-3900000000-c8a10ccf06e1cb8b548a	JSpectraViewer
MS	Mass Spectrum (Electron Ionization)	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer

References

References:

Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
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
Dunn, C. A., O'Handley, S. F., Frick, D. N., Bessman, M. J. (1999). "Studies on the ADP-ribose pyrophosphatase subfamily of the nudix hydrolases and tentative identification of trgB, a gene associated with tellurite resistance." J Biol Chem 274:32318-32324.10542272
Belenky, P., Racette, F. G., Bogan, K. L., McClure, J. M., Smith, J. S., Brenner, C. (2007). "Nicotinamide riboside promotes Sir2 silencing and extends lifespan via Nrk and Urh1/Pnp1/Meu1 pathways to NAD+." Cell 129:473-484.17482543

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	16960
HMDB ID	Not Available
Pubchem Compound ID	49791950
Kegg ID	C00301
ChemSpider ID	30975
FOODB ID	Not Available
Wikipedia	Adenosine_diphosphate_ribose
BioCyc ID	ADENOSINE_DIPHOSPHATE_RIBOSE

Enzymes

Protein Details

1. ADP-ribose pyrophosphatase

General function:: Involved in hydrolase activity
Specific function:: ADP-ribose + H(2)O = AMP + D-ribose 5- phosphate
Gene Name:: YSA1
Uniprot ID:: Q01976
Molecular weight:: 26086.80078

Reactions

ADP-ribose + H(2)O → AMP + D-ribose 5-phosphate.

Structure for #<Compound:0xb3c6f0bc>

Enzymes

Reactions