Guanosine 3',5'-bis(diphosphate) (PAMDB001005)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB001005
Identification
Name: Guanosine 3',5'-bis(diphosphate)
Description:(p)ppGpp, guanosine pentaphosphate or tetraphosphate is an alarmone which is involved in the stringent response in bacteria, causing the inhibition of RNA synthesis when there is a shortage of amino acids present. This causes translation to decrease and the amino acids present are therefore conserved. (p)ppGpp is an effector molecule which is produced as a result of amino acid starvation within a bacterial cell.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • Guanosine 3',5'-bis(diphosphate)
  • Guanosine 3',5'-bis(diphosphoric acid)
  • Guanosine 3',5'-bis(trihydrogen diphosphate)
  • Guanosine 3',5'-bis(trihydrogen diphosphoric acid)
  • Guanosine 3',5'-bispyrophosphate
  • Guanosine 3',5'-bispyrophosphoric acid
  • Guanosine 3'-diphosphate 5'-diphosphate
  • Guanosine 3'-diphosphoric acid 5'-diphosphoric acid
  • Guanosine 5'-diphosphate,3'-diphosphate
  • Guanosine 5'-diphosphoric acid,3'-diphosphoric acid
  • Guanosine tetraphosphate
  • Guanosine tetraphosphoric acid
  • GUANOSINE-5',3'-TETRAPHOSPHATE
  • GUANOSINE-5',3'-tetraphosphoric acid
  • Magic spot
  • Magic spot I
  • Ppgpp
Chemical Formula: C10H17N5O17P4
Average Molecular Weight: 603.1603
Monoisotopic Molecular Weight: 602.956990191
InChI Key: BUFLLCUFNHESEH-UUOKFMHZSA-N
InChI:InChI=1S/C10H17N5O17P4/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(30-36(26,27)32-34(21,22)23)3(29-9)1-28-35(24,25)31-33(18,19)20/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
CAS number: 33503-72-9
IUPAC Name:{[hydroxy({[(2R,3S,4R,5R)-4-hydroxy-2-({[hydroxy(phosphonooxy)phosphoryl]oxy}methyl)-5-(6-hydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)oxolan-3-yl]oxy})phosphoryl]oxy}phosphonic acid
Traditional IUPAC Name: {hydroxy[(2R,3S,4R,5R)-4-hydroxy-2-({[hydroxy(phosphonooxy)phosphoryl]oxy}methyl)-5-(6-hydroxy-2-imino-3H-purin-9-yl)oxolan-3-yl]oxyphosphoryl}oxyphosphonic acid
SMILES:[H][C@]1(COP(O)(=O)OP(O)(O)=O)O[C@@]([H])(N2C=NC3=C2NC(=N)N=C3O)[C@]([H])(O)[C@]1([H])OP(O)(=O)OP(O)(O)=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Purine nucleotides
Sub ClassPurine ribonucleotides
Direct Parent Purine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine ribonucleoside diphosphate
  • Purine ribonucleoside 3',5'-bisphosphate
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Purine
  • Imidazopyrimidine
  • Hydroxypyrimidine
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Pyrimidine
  • 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
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular Framework Aromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State: Not Available
Charge:-5
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility10.3 mg/mLALOGPS
logP-0.5ALOGPS
logP-3.9ChemAxon
logS-1.8ALOGPS
pKa (Strongest Acidic)1.46ChemAxon
pKa (Strongest Basic)7.15ChemAxon
Physiological Charge-5ChemAxon
Hydrogen Acceptor Count17ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area342.33 Å2ChemAxon
Rotatable Bond Count10ChemAxon
Refractivity118.69 m3·mol-1ChemAxon
Polarizability44.68 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Adenosine triphosphate + Guanosine diphosphate > Adenosine monophosphate + Hydrogen ion + Guanosine 3',5'-bis(diphosphate)
Water + Guanosine 3',5'-bis(diphosphate) <> Guanosine diphosphate + Pyrophosphate
Guanosine 3'-diphosphate 5'-triphosphate + Water <> Guanosine 3',5'-bis(diphosphate) + Phosphate
Adenosine triphosphate + Guanosine diphosphate > Adenosine monophosphate + Guanosine 3',5'-bis(diphosphate)
Guanosine 3',5'-bis(diphosphate) + Water > Hydrogen ion + Pyrophosphate + Guanosine diphosphate
Water + Guanosine 3'-diphosphate 5'-triphosphate > Hydrogen ion + Phosphate + Guanosine 3',5'-bis(diphosphate)
Guanosine 3'-diphosphate 5'-triphosphate + Water > Guanosine 3',5'-bis(diphosphate) + Inorganic phosphate
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0900251000-bee48e0fb5019193ebb1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900110000-1afec092079feefa49a9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-1900000000-a38786c52bb589355d91View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0900026000-a8f89e925338c7ff167dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ke9-4900000000-9b838d812b5a59d56595View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9400000000-7ec14f477759ced2651fView in MoNA
References
References:
  • 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
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID17633
HMDB IDHMDB59638
Pubchem Compound ID439450
Kegg IDC01228
ChemSpider ID388557
Wikipedia IDNot Available
BioCyc IDGUANOSINE-5DP-3DP
EcoCyc IDGUANOSINE-5DP-3DP
Ligand ExpoG4P