8-Oxo-dGMP (YMDB00050)

Identification

YMDB ID

YMDB00050

Name

8-Oxo-dGMP

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

8-Oxo-dGMP, also known as 8OG, belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside monophosphates. These are purine nucleotides with monophosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. 8-Oxo-dGMP is a moderately basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI

Synonyms

8-Oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphate
8OG
{[(3S)-5-(6,8-dihydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonate

CAS number

127027-50-3

Weight

Average: 363.2206
Monoisotopic: 363.057998961

InChI Key

AQIVLFLYHYFRKU-KLFYCJEISA-N

InChI

InChI=1S/C10H14N5O8P/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(23-5)2-22-24(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H2,19,20,21)(H3,11,13,14,17)/t3-,4?,5?/m0/s1

IUPAC Name

{[(3S)-5-(2-amino-6,8-dioxo-6,7,8,9-tetrahydro-3H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional IUPAC Name

[(3S)-5-(2-amino-6,8-dioxo-3,7-dihydropurin-9-yl)-3-hydroxyoxolan-2-yl]methoxyphosphonic acid

Chemical Formula

C₁₀H₁₄N₅O₈P

SMILES

[H]O[C@@]1([H])C([H])([H])C([H])(OC1([H])C([H])([H])OP(=O)(O[H])O[H])N1C(=O)N([H])C2=C1N([H])C(=NC2=O)N([H])[H]

Chemical Taxonomy

Description

belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside monophosphates. These are purine nucleotides with monophosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine deoxyribonucleotides

Direct Parent

Purine 2'-deoxyribonucleoside monophosphates

Alternative Parents

Substituents

Purine 2'-deoxyribonucleoside monophosphate
6-oxopurine
Hypoxanthine
Purinone
Imidazopyrimidine
Purine
Aminopyrimidine
Monoalkyl phosphate
Pyrimidone
N-substituted imidazole
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Pyrimidine
Heteroaromatic compound
Azole
Imidazole
Vinylogous amide
Tetrahydrofuran
Urea
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Azacycle
Organopnictogen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Amine
Organic oxygen compound
Hydrocarbon derivative
Alcohol
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

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	5.97 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-3.6	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	1.28	ChemAxon
pKa (Strongest Basic)	2.59	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	196.04 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	83.57 m³·mol⁻¹	ChemAxon
Polarizability	30.66 Å³	ChemAxon
Number of Rings	3	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

Peroxisome

Organoleptic Properties

Not Available

SMPDB Pathways

Not Available

KEGG Pathways

Not Available

SMPDB Reactions

Not Available

KEGG Reactions

Not Available

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9322000000-a96a87df1eb6a033b2c6	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0002-9220100000-a730acbf06167a837d65	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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014i-0900000000-17afa8db0a103a9d78cf	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014i-0900000000-730d6cf8a8af3b2f4896	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0gb9-0900000000-75da77bef96bdce1d716	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03fr-5209000000-640c16b49b93300fd79f	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9400000000-fe0220f3e0d0d30586b0	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-644bcc4b9ebe6d9229a3	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03xr-0149000000-e56c08bb8b99b0293f4e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014i-0920000000-ccb69db0d7b30b629305	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-014i-1930000000-a2811cea8c32b84be9f0	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-1009000000-9f44f66efd9e707294ff	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9002000000-d9e3a2dca5a81da5a6de	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-f2e971234f651dc6d224	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:

UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	Not Available
HMDB ID	HMDB11670
Pubchem Compound ID	447903
Kegg ID	Not Available
ChemSpider ID	24785542
FOODB ID	FDB028359
Wikipedia ID	Not Available
BioCyc ID	Not Available

Enzymes

Protein Details

1. Peroxisomal coenzyme A diphosphatase 1, peroxisomal

General function:: Involved in hydrolase activity
Specific function:: Coenzyme A diphosphatase which mediates the cleavage of CoA into 3',5'-ADP and 4'-phosphopantetheine. Has a strong preference for oxidized CoA disulfide (CoASSCoA) as substrate. May be required to remove potentially toxic oxidized CoA disulfide to maintain the capacity for beta-oxidation of fatty acids. Can degrade 8-oxo-dGTP in vitro; however, such activity may not be relevant in vivo
Gene Name:: PCD1
Uniprot ID:: Q12524
Molecular weight:: 39754.5

Reactions

8-oxo-dGTP + H(2)O → 8-oxo-dGMP + diphosphate.

Structure for #<Compound:0xacac3b70>

Enzymes

Reactions