Linear dimeric GMP (ECMDB20579) (M2MDB001381)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (9)
Record Information
Version2.0
Creation Date2012-05-31 14:51:38 -0600
Update Date2015-06-03 17:20:20 -0600
Secondary Accession Numbers
  • ECMDB20579
Identification
Name:Linear dimeric GMP
DescriptionLinear dimeric GMP 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.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 5'-Monophosphate-guanylyl-3',5'-guanosine
  • 5'-Monophosphoric acid-guanylyl-3',5'-guanosine
  • 5'-Phosphoguanylyl(3'->5')guanosine
  • 5'PGpG
  • L-Di-GMP
  • Nchembio.136-comp9
Chemical Formula:C20H23N10O15P2
Weight:Average: 705.4021
Monoisotopic: 705.08195814
InChI Key:ZEHOHLFQOXAZHX-MHARETSRSA-K
InChI:InChI=1S/C20H26N10O15P2/c21-19-25-13-7(15(34)27-19)23-3-29(13)17-10(32)9(31)5(43-17)1-42-47(39,40)45-12-6(2-41-46(36,37)38)44-18(11(12)33)30-4-24-8-14(30)26-20(22)28-16(8)35/h3-6,9-12,17-18,31-33H,1-2H2,(H,39,40)(H2,36,37,38)(H3,21,25,27,34)(H3,22,26,28,35)/p-3/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1
CAS number:Not Available
IUPAC Name:9-[(2R,3R,4S,5R)-4-[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-imino-6-oxido-3,9-dihydro-2H-purin-9-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]-5-[(hydrogen phosphonatooxy)methyl]-3-hydroxyoxolan-2-yl]-2-imino-3,9-dihydro-2H-purin-6-olate
Traditional IUPAC Name:9-[(2R,3R,4S,5R)-4-({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-imino-6-oxido-3H-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy)-5-[(hydrogen phosphonatooxy)methyl]-3-hydroxyoxolan-2-yl]-2-imino-3H-purin-6-olate
SMILES:[H][C@]1(COP(O)(=O)O[C@]2([H])[C@@]([H])(COP(O)([O-])=O)O[C@@]([H])(N3C=NC4=C3NC(=N)N=C4[O-])[C@]2([H])O)O[C@@]([H])(N2C=NC3=C2NC(=N)N=C3[O-])[C@]([H])(O)[C@]1([H])O
Chemical Taxonomy
Description belongs to the class of organic compounds known as (3'->5')-dinucleotides. These are dinucleotides where the two bases are connected via a (3'->5')-phosphodiester linkage.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
Class(3'->5')-dinucleotides and analogues
Sub Class(3'->5')-dinucleotides
Direct Parent(3'->5')-dinucleotides
Alternative Parents
Substituents
  • (3'->5')-dinucleotide
  • Purine ribonucleoside 3',5'-bisphosphate
  • Purine ribonucleoside bisphosphate
  • Purine ribonucleoside monophosphate
  • Pentose phosphate
  • Ribonucleoside 3'-phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • 6-oxopurine
  • Hypoxanthine
  • Monosaccharide phosphate
  • Purine
  • Imidazopyrimidine
  • Dialkyl phosphate
  • Pyrimidone
  • Aminopyrimidine
  • Alkyl phosphate
  • Monosaccharide
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Pyrimidine
  • Phosphoric acid ester
  • Tetrahydrofuran
  • Imidazole
  • Azole
  • Heteroaromatic compound
  • Vinylogous amide
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Hydrocarbon derivative
  • Primary amine
  • Amine
  • Organonitrogen compound
  • Organooxygen compound
  • Alcohol
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxide
  • Organic anion
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-3
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility4.56 g/LALOGPS
logP-0.97ALOGPS
logP-4.4ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)1.13ChemAxon
pKa (Strongest Basic)5.16ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count20ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area382.74 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity188.35 m³·mol⁻¹ChemAxon
Polarizability59.93 ųChemAxon
Number of Rings6ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
3',5'-Cyclic diGMP + Water + Cyclic di-3',5'-guanylate <> Linear dimeric GMP
cyclic di-3',5'-guanylate + Water > Hydrogen ion + Linear dimeric GMP
SMPDB Pathways:Not Available
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-1200000900-7865d2d0c39d90ff172dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03dm-6101005900-1af9c7303886660a1026View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0005-9510000000-b6f543c01fb0a5fd4beeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-1000000900-e90e3aa876adfbcb85b2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-003r-9000000200-e3f0a50c54d71833dc20View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-003s-9000000000-ceb3199d29b8721d9623View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
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 ID58754
HMDB IDNot Available
Pubchem Compound ID25093482
Kegg IDC18076
ChemSpider ID24605057
Wikipedia IDNot Available
BioCyc IDL-DI-GMP
EcoCyc IDL-DI-GMP

Enzymes

Protein Details
1. Cyclic di-GMP phosphodiesterase yahA
General function:
Involved in two-component response regulator activity
Specific function:
Hydrolyzes c-di-GMP (cyclic bis(3'-5') dimeric GMP) to 5'-pGpG, known as PDE-A activity. PDE-B activity, that is hydrolysis of 5'-pGpG to GMP, proceeds only very slowly
Gene Name:
yahA
Uniprot ID:
P21514
Molecular weight:
40725
Protein Details
2. Oxygen sensor protein DosP
General function:
Involved in phosphorus-oxygen lyase activity
Specific function:
In association with DosC is involved in the production and removal of the second messenger c-di-GMP in response to changing O(2) levels. Has phosphodiesterase (PDE) activity with c- di-GMP (PubMed:15995192), very poor activity on cAMP (PubMed:15995192) but not with cGMP, bis(p-nitrophenyl) phosphate or p-nitrophenyl phosphate (PubMed:11970957). Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria
Gene Name:
dosP
Uniprot ID:
P76129
Molecular weight:
90260
Reactions
Cyclic di-3',5'-guanylate + H(2)O = 5'-phosphoguanylyl(3'->5')guanosine.