3',5'-cyclic GMP (YMDB00454)

Identification

YMDB ID

YMDB00454

Name

3',5'-cyclic GMP

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Cyclic GMP, also known as CGMP or 3',5'-cyclic GMP, belongs to the class of organic compounds known as 3',5'-cyclic purine nucleotides. These are purine nucleotides in which the oxygen atoms linked to the C3 and C5 carbon atoms of the ribose moiety are both bonded the same phosphorus atom of the phosphate group. Cyclic GMP is a moderately basic compound (based on its pKa). Cyclic GMP exists in all living species, ranging from bacteria to humans.

Structure

MOL SDF PDB SMILES InChI

Synonyms

3',5'-Cyclic GMP
3',5'-guanosine
3',5'-guanosine monophosphate
cGMP
cyclic 3',5'-guanosine monophosphate
cyclic gmp
cyclic guanosine 3',5'-monophosphate
cyclic-GMP
guanosine 3,5-cyclic monophosphate
guanosine 3,5-cyclic phosphate
Guanosine 3',5'-cyclic monophosphate
guanosine 3',5'-cyclic phosphate
guanosine 3',5'-cyclic-monophosphate
guanosine 3',5'-monophosphate
Guanosine cyclic 3',5'-(hydrogen phosphate)
Guanosine cyclic monophosphate
guanosine cyclic-monophosphate
guanosine-cyclic-phosphoric-acid
Guanosine 3',5'-cyclic monophosphoric acid
Guanosine 3',5'-cyclic phosphoric acid
Guanosine cyclic monophosphoric acid
Cyclic 3',5'-monophosphate, guanosine
GMP, Cyclic
Guanosine cyclic-3',5'-monophosphate
monoPhosphate, guanosine cyclic
3',5'-monoPhosphate, guanosine cyclic
Cyclic-3',5'-monophosphate, guanosine
Guanosine cyclic 3',5'-monophosphate
Guanosine cyclic 3,5 monophosphate
Cyclic monophosphate, guanosine
Guanosine cyclic 3',5' monophosphate

CAS number

7665-99-8

Weight

Average: 345.2053
Monoisotopic: 345.047434275

InChI Key

ZOOGRGPOEVQQDX-UUOKFMHZSA-N

InChI

InChI=1S/C10H12N5O7P/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6-3(21-9)1-20-23(18,19)22-6/h2-3,5-6,9,16H,1H2,(H,18,19)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1

IUPAC Name

9-[(4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxo-hexahydro-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-2-amino-6,9-dihydro-1H-purin-6-one

Traditional IUPAC Name

cyclic-GMP

Chemical Formula

C₁₀H₁₂N₅O₇P

SMILES

NC1=NC2=C(N=CN2[C@@H]2O[C@@H]3COP(O)(=O)O[C@H]3[C@H]2O)C(=O)N1

Chemical Taxonomy

Description

belongs to the class of organic compounds known as 3',5'-cyclic purine nucleotides. These are purine nucleotides in which the oxygen atoms linked to the C3 and C5 carbon atoms of the ribose moiety are both bonded the same phosphorus atom of the phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Cyclic purine nucleotides

Direct Parent

3',5'-cyclic purine nucleotides

Alternative Parents

Substituents

3',5'-cyclic purine ribonucleotide
Pentose phosphate
Glycosyl compound
N-glycosyl compound
6-oxopurine
Hypoxanthine
Monosaccharide phosphate
Purinone
Imidazopyrimidine
Purine
Aminopyrimidine
Pyrimidone
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Pyrimidine
Vinylogous amide
Azole
Tetrahydrofuran
Heteroaromatic compound
Imidazole
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Alcohol
Organic nitrogen compound
Organopnictogen compound
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Organic oxide
Primary amine
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

3',5'-cyclic purine nucleotide (CHEBI:16356 )
guanyl ribonucleotide (CHEBI:16356 )
3',5'-Cyclic nuclcleotides (C00942 )

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	3.79 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.1	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	2.05	ChemAxon
pKa (Strongest Basic)	1.41	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	170.52 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	71.72 m³·mol⁻¹	ChemAxon
Polarizability	29.19 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	1	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

Organoleptic Properties

Not Available

SMPDB Pathways

Not Available

KEGG Pathways

Purine metabolism

ec00230

SMPDB Reactions

Not Available

KEGG Reactions

water + 3',5'-cyclic GMP → Guanosine monophosphate + hydron

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-001i-2972000000-80320c485cef8d6d91ad	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-001i-2972000000-80320c485cef8d6d91ad	JSpectraViewer \| MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0f76-3901000000-c970aad6713a547b2d8f	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-00di-4590100000-edbc82f84eca5a64f5a5	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-0uec-2904000000-85af5865e64af24e7691	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-0udi-0904000000-e34bb3204af3b18ddf11	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-0udj-0908000000-35925bce602ee60e24ee	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-0udj-0904000000-93fabfb961527e02671e	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-0udj-0907000000-60b56b2fcc437a04a7b8	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , negative	splash10-0udj-0908000000-16c413e42a41fa5e7262	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-0udl-3904000000-051a745d5db4f607a935	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-0udi-0901000000-a2a6721a5a98c3d3e945	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-0udj-0907000000-ae3d3b4dfb6aefdd34c3	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-0udj-0904000000-fd635f17953dbbff039b	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-0udi-0902000000-36d8b1a240f9f6471886	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-0002-0009000000-4c75be42ba8dbd671bbf	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-0002-0009000000-06ee1dc93418cde4fe39	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-0udi-0900000000-db6612a4a4b92db51507	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-0udi-0900000000-8455683aa1bc0141dd38	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-0udi-0900000000-196c267f58b468d3a8f5	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-0002-0009000000-7637808812023bf3fb33	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-0002-0009000000-34c09019debbbd2ef2a6	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Linear Ion Trap , positive	splash10-0002-0009000000-db049b28da12291887ce	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0904000000-65ab088e129c01a9b140	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900000000-fc45e23a1d622d9a6848	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udr-0900000000-d7d3bc38b1c32086753e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f6x-1709000000-881760c573673e832db8	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-2900000000-f74b8ec55fbea3fdf8cd	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-003u-9600000000-d7f00c8f8cec474c7304	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:

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
Eckstein, H., Flugge, B. (1999). "Guanosine 3':5'-cyclic monophosphate-dependent particulate protein kinase activity from yeast (Saccharomyces cerevisiae)." Z Naturforsch C 54:84-93.10097409

Synthesis Reference:

Sekhar, Konjeti R.; Grondin, Pascal; Francis, Sharron H.; Corbin, Jackie D. Design and synthesis of xanthines and cyclic GMP analogs as potent inhibitors of PDE5. Phosphodiesterase Inhibitors (1996), 135-146.

External Links:

Resource	Link
CHEBI ID	16356
HMDB ID	HMDB01314
Pubchem Compound ID	24316
Kegg ID	C00942
ChemSpider ID	22734
FOODB ID	FDB030764
Wikipedia	Cyclic_guanosine_monophosphate
BioCyc ID	CGMP

Enzymes

Protein Details

1. 3',5'-cyclic-nucleotide phosphodiesterase 2

General function:: Involved in catalytic activity
Specific function:: Controls the level of cAMP in yeast cells, together with the low-affinity cAMP phosphodiesterase (PDE1)
Gene Name:: PDE2
Uniprot ID:: P06776
Molecular weight:: 60999.19922

Reactions

Adenosine 3',5'-cyclic phosphate + H(2)O → adenosine 5'-phosphate.

Structure for #<Compound:0xaf4e9418>

Enzymes

Reactions