MiMeDB: Showing metabocard for N2,N2-Dimethyl-guanosine (MMDBc0013863)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 05:04:03 UTC

Update Date

2025-10-07 16:06:12 UTC

Metabolite ID

MMDBc0013863

Metabolite Identification

Common Name

N2,N2-Dimethyl-guanosine

Description

N2,N2-Dimethyl-guanosine is a modified nucleoside classified as a metabolite, specifically belonging to the class of methylated guanosine derivatives. This compound is of interest in both chemistry and biology due to its role in cellular processes and potential implications in disease states. It has been identified in studies examining the urinary excretion of various nucleosides, including pseudo-uridine, 1-methyl-adenosine, 1-methyl-inosine, 1-methyl-guanosine, and 2-methyl-guanosine, alongside N2,N2-dimethyl-guanosine in patients with breast carcinoma, including those with metastases (PMID:3426126 ). The presence of N2,N2-dimethyl-guanosine in biological fluids may serve as a biomarker for certain pathological conditions, reflecting alterations in nucleoside metabolism associated with cancer. Further research into this compound could elucidate its biological significance and potential applications in clinical diagnostics or therapeutic strategies.

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004261502402D          

 22 24  0  0  0  0            999 V2000
    3.4990    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845   -0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0865   -0.5966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984   -1.2640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -2.0486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6635   -2.2201    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831   -1.0091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505   -1.4940    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831   -0.1841    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505    0.3009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    3.1729    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 11 18  1  0  0  0  0
 18 19  1  0  0  0  0
  7 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
  4 22  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0013863

> <DATABASE_NAME>
MIME

> <SMILES>
CN(C)C1=NC2=C(N=CN2C2OC(CO)C(O)C2O)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C12H17N5O5/c1-16(2)12-14-9-6(10(21)15-12)13-4-17(9)11-8(20)7(19)5(3-18)22-11/h4-5,7-8,11,18-20H,3H2,1-2H3,(H,14,15,21)

> <INCHI_KEY>
RSPURTUNRHNVGF-UHFFFAOYSA-N

> <FORMULA>
C12H17N5O5

> <MOLECULAR_WEIGHT>
311.298

> <EXACT_MASS>
311.122968667

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
30.159413473317727

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
9-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-(dimethylamino)-6,9-dihydro-1H-purin-6-one

> <ALOGPS_LOGP>
-1.40

> <JCHEM_LOGP>
-2.166632731333333

> <ALOGPS_LOGS>
-1.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.456070987464837

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.961355776323558

> <JCHEM_PKA_STRONGEST_BASIC>
0.5133916941782972

> <JCHEM_POLAR_SURFACE_AREA>
132.44000000000003

> <JCHEM_REFRACTIVITY>
74.6904

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.56e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-(dimethylamino)-1H-purin-6-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-APR-15         0                                  
HETATM    1  C   UNK     0       6.531   2.073   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       5.198   1.303   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       5.198  -0.237   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.864   2.073   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       2.530   1.303   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.197   2.073   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.197   3.613   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -0.268   4.089   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      -1.173   2.843   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -0.268   1.597   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -0.744   0.132   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.161  -1.114   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.744  -2.359   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.268  -3.824   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.238  -4.144   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -2.208  -1.884   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -3.454  -2.789   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -2.208  -0.344   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -3.454   0.562   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       2.530   4.383   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       2.530   5.923   0.000  0.00  0.00           O+0
HETATM   22  N   UNK     0       3.864   3.613   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   22                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   10                                                  
CONECT    7    6    8   20                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    6   11                                                  
CONECT   11   10   12   18                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   13   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   11   19                                                  
CONECT   19   18                                                            
CONECT   20    7   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20    4                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

Synonyms

Not Available

Molecular Formula

C₁₂H₁₇N₅O₅

Average Mass

311.298

Monoisotopic Mass

311.122968667

IUPAC Name

9-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-(dimethylamino)-6,9-dihydro-1H-purin-6-one

Traditional Name

9-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-(dimethylamino)-1H-purin-6-one

CAS Registry Number

Not Available

SMILES

CN(C)C1=NC2=C(N=CN2C2OC(CO)C(O)C2O)C(=O)N1

InChI Identifier

InChI=1S/C12H17N5O5/c1-16(2)12-14-9-6(10(21)15-12)13-4-17(9)11-8(20)7(19)5(3-18)22-11/h4-5,7-8,11,18-20H,3H2,1-2H3,(H,14,15,21)

InChI Key

RSPURTUNRHNVGF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Not Available

Direct Parent

Purine nucleosides

Alternative Parents

Substituents

Purine nucleoside
Glycosyl compound
N-glycosyl compound
6-oxopurine
Hypoxanthine
Pentose monosaccharide
Purinone
Imidazopyrimidine
Purine
Dialkylarylamine
Pyrimidone
Aminopyrimidine
Pyrimidine
N-substituted imidazole
Monosaccharide
Vinylogous amide
Tetrahydrofuran
Heteroaromatic compound
Azole
Imidazole
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Organic nitrogen compound
Hydrocarbon derivative
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Primary alcohol
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	15.6 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-2.2	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	9.96	ChemAxon
pKa (Strongest Basic)	0.51	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	132.44 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	74.69 m³·mol⁻¹	ChemAxon
Polarizability	30.16 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank	Species

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Firmicutes	1	Human ; Human feces; Human saliva; Human mucosa	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

601633

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for N2,N2-Dimethyl-guanosine (MMDBc0013863)

MOL for #<Metabolite:0x00007f2af4c70d50>

3D MOL for #<Metabolite:0x00007f2af4c70d50>

3D SDF for #<Metabolite:0x00007f2af4c70d50>

3D-SDF for #<Metabolite:0x00007f2af4c70d50>

PDB for #<Metabolite:0x00007f2af4c70d50>

3D PDB for #<Metabolite:0x00007f2af4c70d50>

SMILES for #<Metabolite:0x00007f2af4c70d50>

INCHI for #<Metabolite:0x00007f2af4c70d50>

Structure for #<Metabolite:0x00007f2af4c70d50>

3D Structure for #<Metabolite:0x00007f2af4c70d50>