Guanosine 3'-diphosphate 5'-triphosphate (PAMDB001003)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB001003
Identification
Name: Guanosine 3'-diphosphate 5'-triphosphate
Description:Guanosine 3'-diphosphate 5'-triphosphate is a member of the chemical class 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. The hallmark of the stringent response is the accumulation of guanosine tetra- (ppGpp) and pentaphosphates (pppGpp), which probably bind RNA polymerase to regulate gene expression at certain promoters. (PMID 11282471) Guanosine 5'-triphosphate 3'-diphosphate (pppGpp) and guanosine 5'-diphosphate 3'-diphosphate (ppGpp) are specifically degraded by a manganese-dependent pyrophosphorylase present in spoT+ but not in spoT- strains of Pseudomonas aeruginosa, indicating that the enzyme is the spoT gene product. (PMID 365225) The kinetics of the GTP level during starvation suggests that GTP is a precursor of pppGpp. (PMID 793688)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • Guanosine 3'-diphosphate 5'-triphosphate
  • Guanosine 3'-diphosphoric acid 5'-triphosphoric acid
  • Guanosine 5'-triphosphate,3'-diphosphate
  • Guanosine 5'-triphosphoric acid,3'-diphosphoric acid
  • Guanosine pentaphosphate
  • Guanosine pentaphosphoric acid
  • Magic spot
  • Pppgpp
Chemical Formula: C10H18N5O20P5
Average Molecular Weight: 683.1402
Monoisotopic Molecular Weight: 682.923320601
InChI Key: KCPMACXZAITQAX-UUOKFMHZSA-N
InChI:InChI=1S/C10H18N5O20P5/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(32-39(26,27)33-36(18,19)20)3(31-9)1-30-38(24,25)35-40(28,29)34-37(21,22)23/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H,28,29)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
CAS number: 38918-96-6
IUPAC Name:{[hydroxy({[(2R,3S,4R,5R)-4-hydroxy-2-({[hydroxy({[hydroxy(phosphonooxy)phosphoryl]oxy})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-5-(6-hydroxy-2-imino-3H-purin-9-yl)-2-[({hydroxy[hydroxy(phosphonooxy)phosphoryl]oxyphosphoryl}oxy)methyl]oxolan-3-yl]oxyphosphoryl}oxyphosphonic acid
SMILES:[H][C@]1(COP(O)(=O)OP(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 triphosphates. These are purine ribobucleotides with a triphosphate group linked to the ribose moiety.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Purine nucleotides
Sub ClassPurine ribonucleotides
Direct Parent Purine ribonucleoside triphosphates
Alternative Parents
Substituents
  • Purine ribonucleoside triphosphate
  • 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:-6
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility16.8 mg/mLALOGPS
logP0.16ALOGPS
logP-3.5ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)0.84ChemAxon
Physiological Charge-6ChemAxon
Hydrogen Acceptor Count19ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area388.86 Å2ChemAxon
Rotatable Bond Count12ChemAxon
Refractivity129.57 m3·mol-1ChemAxon
Polarizability49.15 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 triphosphate <> Adenosine monophosphate + Guanosine 3'-diphosphate 5'-triphosphate + Hydrogen ion
Guanosine 3'-diphosphate 5'-triphosphate + Water > Guanosine triphosphate + Pyrophosphate
Adenosine triphosphate + Guanosine triphosphate <> Adenosine monophosphate + Guanosine 3'-diphosphate 5'-triphosphate
Guanosine 3'-diphosphate 5'-triphosphate + Water <> Guanosine 3',5'-bis(diphosphate) + Phosphate
Water + Guanosine 3'-diphosphate 5'-triphosphate > Hydrogen ion + Phosphate + Guanosine 3',5'-bis(diphosphate)
Guanosine 3'-diphosphate 5'-triphosphate + Water > Hydrogen ion + Guanosine triphosphate + Pyrophosphate
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-0900044000-e96c10f40cd9e086d540View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900020000-b82fa0d9a9f331aa2a4bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-1900000000-baf8b81708e533b98dcbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f89-0720009000-1a3224060ede9e590dffView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0zir-5930000000-c118ece248c4154dc94aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-056r-8920000000-f5ca09c09ff793adde1fView in MoNA
References
References:
  • Chaloner-Larsson, G., Yamazaki, H. (1976). "Synthesis of guanosine 5'-triphosphate,3'-diphosphate in a spo T strain of Escherichia coli." Can J Biochem 54:935-940. Pubmed: 793688
  • Chatterji, D., Ojha, A. K. (2001). "Revisiting the stringent response, ppGpp and starvation signaling." Curr Opin Microbiol 4:160-165. Pubmed: 11282471
  • Heinemeyer, E. A., Richter, D. (1978). "Characterization of the guanosine 5'-triphosphate 3'-diphosphate and guanosine 5'-diphosphate 3'-diphosphate degradation reaction catalyzed by a specific pyrophosphorylase from Escherichia coli." Biochemistry 17:5368-5372. Pubmed: 365225
  • 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
  • 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
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID16690
HMDB IDHMDB60480
Pubchem Compound ID38166
Kegg IDC04494
ChemSpider ID34987
Wikipedia IDNot Available
BioCyc IDGDP-TP
EcoCyc IDGDP-TP
Ligand Expo0O2