MiMeDB: Showing metabocard for N2-methyl-guanosine (MMDBc0013282)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 04:37:11 UTC

Update Date

2022-08-31 06:35:50 UTC

Metabolite ID

MMDBc0013282

Metabolite Identification

Common Name

N2-methyl-guanosine

Description

2-[6-hydroxy-2-(methylimino)-3,9-dihydro-2H-purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol 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. 2-[6-hydroxy-2-(methylimino)-3,9-dihydro-2H-purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004171516592D          

 21 23  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
    2.0701    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
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  5  9  1  0  0  0  0
  9 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
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 10 17  1  0  0  0  0
 17 18  1  0  0  0  0
  6 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
  3 21  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0013282

> <DATABASE_NAME>
MIME

> <SMILES>
CNC1=NC2=C(N=CN2C2OC(CO)C(O)C2O)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C11H15N5O5/c1-12-11-14-8-5(9(20)15-11)13-3-16(8)10-7(19)6(18)4(2-17)21-10/h3-4,6-7,10,17-19H,2H2,1H3,(H2,12,14,15,20)

> <INCHI_KEY>
SLEHROROQDYRAW-UHFFFAOYSA-N

> <FORMULA>
C11H15N5O5

> <MOLECULAR_WEIGHT>
297.271

> <EXACT_MASS>
297.107318603

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
28.04710973634858

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.68

> <JCHEM_LOGP>
-2.4286087969999994

> <ALOGPS_LOGS>
-1.36

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.45640935154439

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.058462386299748

> <JCHEM_PKA_STRONGEST_BASIC>
0.46092635006854793

> <JCHEM_POLAR_SURFACE_AREA>
141.23000000000002

> <JCHEM_REFRACTIVITY>
69.39569999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.30e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-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       3.864   2.073   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.530   1.303   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.197   2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.197   3.613   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -0.268   4.089   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -1.173   2.843   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -0.268   1.597   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      -0.744   0.132   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.161  -1.114   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.744  -2.359   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.268  -3.824   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       1.238  -4.144   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -2.208  -1.884   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -3.454  -2.789   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -2.208  -0.344   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -3.454   0.562   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       2.530   4.383   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       2.530   5.923   0.000  0.00  0.00           O+0
HETATM   21  N   UNK     0       3.864   3.613   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   21                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    9                                                  
CONECT    6    5    7   19                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    5   10                                                  
CONECT   10    9   11   17                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   10   18                                                  
CONECT   18   17                                                            
CONECT   19    6   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19    3                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

Synonyms

Not Available

Molecular Formula

C₁₁H₁₅N₅O₅

Average Mass

297.271

Monoisotopic Mass

297.107318603

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

CNC1=NC2=C(N=CN2C2OC(CO)C(O)C2O)C(=O)N1

InChI Identifier

InChI=1S/C11H15N5O5/c1-12-11-14-8-5(9(20)15-11)13-3-16(8)10-7(19)6(18)4(2-17)21-10/h3-4,6-7,10,17-19H,2H2,1H3,(H2,12,14,15,20)

InChI Key

SLEHROROQDYRAW-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
Aminopyrimidine
Secondary aliphatic/aromatic amine
Pyrimidone
Monosaccharide
N-substituted imidazole
Pyrimidine
Azole
Imidazole
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Secondary amine
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Primary alcohol
Organic oxygen compound
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	13 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-2.4	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	10.06	ChemAxon
pKa (Strongest Basic)	0.46	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	141.23 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	69.4 m³·mol⁻¹	ChemAxon
Polarizability	28.05 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

Not Available

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

Metabolic Reactions

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

533562

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

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-methyl-guanosine (MMDBc0013282)

MOL for #<Metabolite:0x00005645c84ad8a0>

3D MOL for #<Metabolite:0x00005645c84ad8a0>

3D SDF for #<Metabolite:0x00005645c84ad8a0>

3D-SDF for #<Metabolite:0x00005645c84ad8a0>

PDB for #<Metabolite:0x00005645c84ad8a0>

3D PDB for #<Metabolite:0x00005645c84ad8a0>

SMILES for #<Metabolite:0x00005645c84ad8a0>

INCHI for #<Metabolite:0x00005645c84ad8a0>

Structure for #<Metabolite:0x00005645c84ad8a0>

3D Structure for #<Metabolite:0x00005645c84ad8a0>