ECMDB: Guanosine 3',5'-bis(diphosphate) (ECMDB20158) (M2MDB001005)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (4)XML

Proteins (487)

Record Information

Version

2.0

Creation Date

2012-05-31 14:30:32 -0600

Update Date

2015-06-03 17:19:25 -0600

Secondary Accession Numbers

ECMDB20158

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

MOL SDF 3D-SDF PDB SMILES InChI View 3D 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

Weight:

Average: 603.1603
Monoisotopic: 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

Description

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 Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine ribonucleotides

Direct Parent

Purine ribonucleoside diphosphates

Alternative Parents

Substituents

Purine ribonucleoside 3',5'-bisphosphate
Purine ribonucleoside bisphosphate
Purine ribonucleoside diphosphate
Ribonucleoside 3'-phosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
6-oxopurine
Hypoxanthine
Monosaccharide phosphate
Organic pyrophosphate
Imidazopyrimidine
Purine
Aminopyrimidine
Monoalkyl phosphate
Pyrimidone
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Tetrahydrofuran
Vinylogous amide
Azole
Imidazole
Heteroaromatic compound
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Hydrocarbon derivative
Amine
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Primary amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

guanosine bisphosphate (CHEBI:17633 )

Physical Properties

State:

Not Available

Charge:

-5

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	10.3 g/L	ALOGPS
logP	-0.5	ALOGPS
logP	-3.9	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	1.46	ChemAxon
pKa (Strongest Basic)	7.15	ChemAxon
Physiological Charge	-5	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	342.33 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	118.69 m³·mol⁻¹	ChemAxon
Polarizability	44.68 Å³	ChemAxon
Number of Rings	3	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:

Cytoplasm

Reactions:

SMPDB Pathways:

Not Available

KEGG Pathways:

Purine metabolism ec00230

EcoCyc Pathways:

ppGpp biosynthesis PPGPPMET-PWY

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-4903440000-3e191d1a58e267ff9c41	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0002-8252953000-fd50d9797f6f347aea0e	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_16) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0900251000-bee48e0fb5019193ebb1	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900110000-1afec092079feefa49a9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-1900000000-a38786c52bb589355d91	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0900026000-a8f89e925338c7ff167d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0ke9-4900000000-9b838d812b5a59d56595	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9400000000-7ec14f477759ced2651f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0000009000-999a2f925527a6d08b61	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-2104394000-4e37a899d52d7d01266a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000020000-b576b2a8534ffd50db68	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0800009000-7b596564eaa6441fcd1a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0uk9-0800391000-5e4592414d4a55653d2f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0w30-1796200000-2948cd2c228e6a5aa92c	View in MoNA
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View 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

Links

External Links:

Resource	Link
CHEBI ID	17633
HMDB ID	HMDB0059638
Pubchem Compound ID	439450
Kegg ID	C01228
ChemSpider ID	388557
Wikipedia ID	Not Available
BioCyc ID	GUANOSINE-5DP-3DP
EcoCyc ID	GUANOSINE-5DP-3DP
Ligand Expo	G4P

Enzymes

Protein Details

1. Exopolyphosphatase

General function:: Involved in magnesium ion binding
Specific function:: Degradation of inorganic polyphosphates. Orthophosphate is released progressively from the ends of polyphosphate of circa 500 residues long, while chains of circa 15 residues compete poorly with polyphosphate as substrate
Gene Name:: ppx
Uniprot ID:: P0AFL6
Molecular weight:: 58136

Reactions

(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate.

Protein Details

2. GTP pyrophosphokinase

General function:: Involved in amino acid binding
Specific function:: In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance. This enzyme catalyzes the formation of pppGpp which is then hydrolyzed to form ppGpp
Gene Name:: relA
Uniprot ID:: P0AG20
Molecular weight:: 83875

Reactions

ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate.

Protein Details

3. Bifunctional (p)ppGpp synthase/hydrolase SpoT

General function:: Involved in catalytic activity
Specific function:: In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance. This enzyme catalyzes both the synthesis and degradation of ppGpp. The second messengers ppGpp and c-di-GMP together control biofilm formation in response to translational stress; ppGpp represses biofilm formation while c- di-GMP induces it
Gene Name:: spoT
Uniprot ID:: P0AG24
Molecular weight:: 79342

Reactions

ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate.
Guanosine 3',5'-bis(diphosphate) + H(2)O = guanosine 5'-diphosphate + diphosphate.

Protein Details

4. Guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase

General function:: Involved in guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity
Specific function:: Conversion of pppGpp to ppGpp. Guanosine pentaphosphate (pppGpp) is a cytoplasmic signaling molecule which together with ppGpp controls the "stringent response", an adaptive process that allows bacteria to respond to amino acid starvation, resulting in the coordinated regulation of numerous cellular activities
Gene Name:: gppA
Uniprot ID:: P25552
Molecular weight:: 54871

Reactions

Guanosine 5'-triphosphate,3'-diphosphate + H(2)O = guanosine 3',5'-bis(diphosphate) + phosphate.

Guanosine 3',5'-bis(diphosphate) (ECMDB20158) (M2MDB001005)

Structure for #<Compound:0xa2661550>

Enzymes

Reactions

Reactions

Reactions

Reactions