MiMeDB: Showing metabocard for N6,N6-Dimethyladenosine (MMDBc0000728)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:53:40 UTC

Update Date

2022-08-31 06:11:40 UTC

Metabolite ID

MMDBc0000728

Metabolite Identification

Common Name

N6,N6-Dimethyladenosine

Description

N(6),N(6)-dimethyladenosine, also known as 6-(dimethylamino)purine riboside, 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. N(6),N(6)-dimethyladenosine is a strong basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304021923592D          

 25 27  0  0  1  0            999 V2000
    3.3523    3.5854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    3.5854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.4940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -1.0091    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -1.2640    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3687   -0.5966    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4820   -2.3145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -2.0486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -0.5966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -0.1841    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4991   -1.7306    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5351   -2.0117    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7432   -1.3316    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6986    0.1999    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  3  1  1  0  0  0
  8  6  1  0  0  0  0
  9  8  1  0  0  0  0
 10  7  2  0  0  0  0
 11  7  1  0  0  0  0
 12  9  1  0  0  0  0
 13  4  2  0  0  0  0
 13 10  1  0  0  0  0
 14  4  1  0  0  0  0
 14 11  2  0  0  0  0
 15  5  2  0  0  0  0
 15  7  1  0  0  0  0
 16  1  1  0  0  0  0
 16  2  1  0  0  0  0
 16 10  1  0  0  0  0
 17  5  1  0  0  0  0
 17 11  1  0  0  0  0
 12 17  1  1  0  0  0
 18  3  1  0  0  0  0
  8 19  1  6  0  0  0
  9 20  1  6  0  0  0
 21  6  1  0  0  0  0
 21 12  1  0  0  0  0
  6 22  1  6  0  0  0
  8 23  1  1  0  0  0
  9 24  1  1  0  0  0
 12 25  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000728

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CO)O[C@@]([H])(N2C=NC3=C(N=CN=C23)N(C)C)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C12H17N5O4/c1-16(2)10-7-11(14-4-13-10)17(5-15-7)12-9(20)8(19)6(3-18)21-12/h4-6,8-9,12,18-20H,3H2,1-2H3/t6-,8-,9-,12-/m1/s1

> <INCHI_KEY>
WVGPGNPCZPYCLK-WOUKDFQISA-N

> <FORMULA>
C12H17N5O4

> <MOLECULAR_WEIGHT>
295.2945

> <EXACT_MASS>
295.128054057

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
29.30958332528202

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5R)-2-[6-(dimethylamino)-9H-purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol

> <ALOGPS_LOGP>
-0.58

> <JCHEM_LOGP>
-1.1539940589999995

> <ALOGPS_LOGS>
-1.33

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.89122602142637

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.454003633777091

> <JCHEM_PKA_STRONGEST_BASIC>
3.6247795214399137

> <JCHEM_POLAR_SURFACE_AREA>
116.76000000000002

> <JCHEM_REFRACTIVITY>
72.9238

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.39e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N6-dimethyladenosine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-APR-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-APR-19         0                                  
HETATM    1  C   UNK     0       6.258   6.693   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.590   6.693   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.061  -2.789   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.185  -1.884   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.650  -2.359   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.555  -1.114   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       6.258   3.613   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       4.924   1.303   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       4.924   5.923   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0      -0.900  -4.320   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.126  -3.824   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       4.095  -1.114   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.185  -0.344   0.000  0.00  0.00           O+0
HETATM   22  H   UNK     0       0.932  -3.230   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       0.999  -3.755   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       3.254  -2.486   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       3.171   0.373   0.000  0.00  0.00           H+0
CONECT    1   16                                                            
CONECT    2   16                                                            
CONECT    3    6   18                                                       
CONECT    4   13   14                                                       
CONECT    5   15   17                                                       
CONECT    6    3    8   21   22                                             
CONECT    7   10   11   15                                                  
CONECT    8    6    9   19   23                                             
CONECT    9    8   12   20   24                                             
CONECT   10    7   13   16                                                  
CONECT   11    7   14   17                                                  
CONECT   12    9   17   21   25                                             
CONECT   13    4   10                                                       
CONECT   14    4   11                                                       
CONECT   15    5    7                                                       
CONECT   16    1    2   10                                                  
CONECT   17    5   11   12                                                  
CONECT   18    3                                                            
CONECT   19    8                                                            
CONECT   20    9                                                            
CONECT   21    6   12                                                       
CONECT   22    6                                                            
CONECT   23    8                                                            
CONECT   24    9                                                            
CONECT   25   12                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

Synonyms

Value	Source
6-(Dimethylamino)purine ribonucleoside	ChEBI
6-(Dimethylamino)purine riboside	ChEBI
6-Dimethyladenosine	ChEBI
6-Dimethylaminopurine D-riboside	ChEBI
6-N-Dimethyladenosine	ChEBI
N,N-Dimethyladenosine	ChEBI
N6,N6-Dimethyladenosine	ChEBI
N6-Dimethyladenosine	ChEBI
6-Dimethylaminopurine riboside	MeSH
6-(gamma,gamma-dimethylamino)Purine riboside	MeSH
N(6),N(6)-Dimethyladenosine	MeSH

Molecular Formula

C₁₂H₁₇N₅O₄

Average Mass

295.2945

Monoisotopic Mass

295.128054057

IUPAC Name

(2R,3R,4S,5R)-2-[6-(dimethylamino)-9H-purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol

Traditional Name

N6-dimethyladenosine

CAS Registry Number

Not Available

SMILES

[H][C@]1(CO)O[C@@]([H])(N2C=NC3=C(N=CN=C23)N(C)C)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C12H17N5O4/c1-16(2)10-7-11(14-4-13-10)17(5-15-7)12-9(20)8(19)6(3-18)21-12/h4-6,8-9,12,18-20H,3H2,1-2H3/t6-,8-,9-,12-/m1/s1

InChI Key

WVGPGNPCZPYCLK-WOUKDFQISA-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-alkylaminopurine
6-aminopurine
Pentose monosaccharide
Imidazopyrimidine
Purine
Dialkylarylamine
Aminopyrimidine
Monosaccharide
N-substituted imidazole
Imidolactam
Pyrimidine
Azole
Imidazole
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Azacycle
Oxacycle
Organoheterocyclic compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Alcohol
Hydrocarbon derivative
Organopnictogen compound
Organic nitrogen compound
Primary alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

methyladenosine (CHEBI:28284 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	13.9 g/L	ALOGPS
logP	-0.58	ALOGPS
logP	-1.2	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	12.45	ChemAxon
pKa (Strongest Basic)	3.62	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	116.76 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	72.92 m³·mol⁻¹	ChemAxon
Polarizability	29.31 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	3	Human ; Human feces; Human supragingival plaque; Human subgingival plaque; Human saliva; Human urine; Human sputum	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria/Eubacteria	Bacteroidetes	1	Human ; Human feces	Indirect association between microbiota composition and metabolites measured in host biospecimen

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

HMDB0240321

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

C03416

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440004

PDB ID

Not Available

ChEBI ID

28284

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Showing metabocard for N6,N6-Dimethyladenosine (MMDBc0000728)

MOL for #<Metabolite:0x00007f91f7a3d6b8>

3D MOL for #<Metabolite:0x00007f91f7a3d6b8>

3D SDF for #<Metabolite:0x00007f91f7a3d6b8>

3D-SDF for #<Metabolite:0x00007f91f7a3d6b8>

PDB for #<Metabolite:0x00007f91f7a3d6b8>

3D PDB for #<Metabolite:0x00007f91f7a3d6b8>

SMILES for #<Metabolite:0x00007f91f7a3d6b8>

INCHI for #<Metabolite:0x00007f91f7a3d6b8>

Structure for #<Metabolite:0x00007f91f7a3d6b8>

3D Structure for #<Metabolite:0x00007f91f7a3d6b8>