MiMeDB: Showing metabocard for 2'-amino-2'-deoxyguanosine (MMDBc0007409)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 00:36:06 UTC

Update Date

2025-10-07 16:05:19 UTC

Metabolite ID

MMDBc0007409

Metabolite Identification

Common Name

2'-amino-2'-deoxyguanosine

Description

2'-amino-2'-deoxyguanosine is a nucleoside analog belonging to the class of modified deoxynucleosides. It serves as a metabolite with significant implications in biochemical research, particularly in the study of ribozymes and RNA splicing. This compound has been utilized as a probe to investigate metal ion interactions at the active site of group I ribozymes (PMID:17629287 ). Advances in its synthesis have led to improved protocols for obtaining 2'-amino-2'-deoxyguanosine and its phosphoramidite derivatives, enhancing the efficiency and yield of its incorporation into oligonucleotides (PMID:16202607 ). Notably, 2'-amino-2'-deoxyguanosine acts as a cofactor in self-splicing reactions, effectively replacing guanosine in certain ribozymes, although its catalytic efficiency can be lower compared to unmodified counterparts (PMID:1550590 , PMID:1736306 ). The presence of metal ions, such as Mn2+ or Zn2+, has been shown to enhance the transesterification reactions involving this compound (PMID:9016608 ). Overall, 2'-amino-2'-deoxyguanosine is a crucial component in understanding RNA catalysis and the mechanisms of ribozymes.

Structure

MOL SDF PDB SMILES InChI

2'-amino-2'-deoxyguanosine
  Mrv1652309232003592D          

 20 22  0  0  0  0            999 V2000
    0.7018    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2169    0.6674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5678    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5678   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2169   -0.6674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4718   -1.4521    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2564   -1.7070    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2564   -2.5320    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4718   -2.7870    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0131   -2.1195    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2169   -3.5715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5901   -3.7431    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9238   -3.0169    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9238   -1.2221    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2822   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9967   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9967    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2822    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2822    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7112   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  1  0  0  0
 11 12  1  0  0  0  0
  8 13  1  6  0  0  0
  7 14  1  6  0  0  0
  4 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 16 20  1  0  0  0  0
  5  1  1  0  0  0  0
 18  3  1  0  0  0  0
 10  6  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0007409

> <DATABASE_NAME>
MIME

> <SMILES>
N[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=NC2=C1N=C(N)NC2=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H14N6O4/c11-4-6(18)3(1-17)20-9(4)16-2-13-5-7(16)14-10(12)15-8(5)19/h2-4,6,9,17-18H,1,11H2,(H3,12,14,15,19)/t3-,4-,6-,9-/m1/s1

> <INCHI_KEY>
ROPTVRLUGSPXNH-DXTOWSMRSA-N

> <FORMULA>
C10H14N6O4

> <MOLECULAR_WEIGHT>
282.26

> <EXACT_MASS>
282.107652955

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
26.477125304681216

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-9-[(2R,3R,4S,5R)-3-amino-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-6,9-dihydro-1H-purin-6-one

> <ALOGPS_LOGP>
-2.18

> <JCHEM_LOGP>
-2.813099992666667

> <ALOGPS_LOGS>
-1.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.37586343567115

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.161317431732497

> <JCHEM_PKA_STRONGEST_BASIC>
8.048126955491249

> <JCHEM_POLAR_SURFACE_AREA>
161.01000000000002

> <JCHEM_REFRACTIVITY>
66.27859999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.12e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-amino-9-[(2R,3R,4S,5R)-3-amino-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1H-purin-6-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 2'-amino-2'-deoxyguanosine                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-SEP-20         0                                  
HETATM    1  C   UNK     0       1.310   0.000   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       0.405   1.246   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -1.060   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.060  -0.770   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       0.405  -1.246   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       0.881  -2.711   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.345  -3.186   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.345  -4.726   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.881  -5.202   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.025  -3.956   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.405  -6.667   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.102  -6.987   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       3.591  -5.632   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0       3.591  -2.281   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0      -2.393  -1.540   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      -3.727  -0.770   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      -3.727   0.770   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      -2.393   1.540   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -2.393   3.080   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0      -5.061  -1.540   0.000  0.00  0.00           N+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   18                                                  
CONECT    4    3    5   15                                                  
CONECT    5    4    6    1                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    8   14                                                  
CONECT    8    7    9   13                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9    6                                                       
CONECT   11    9   12                                                       
CONECT   12   11                                                            
CONECT   13    8                                                            
CONECT   14    7                                                            
CONECT   15    4   16                                                       
CONECT   16   15   17   20                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19    3                                                  
CONECT   19   18                                                            
CONECT   20   16                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

Synonyms

Not Available

Molecular Formula

C₁₀H₁₄N₆O₄

Average Mass

282.26

Monoisotopic Mass

282.107652955

IUPAC Name

2-amino-9-[(2R,3R,4S,5R)-3-amino-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-6,9-dihydro-1H-purin-6-one

Traditional Name

2-amino-9-[(2R,3R,4S,5R)-3-amino-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1H-purin-6-one

CAS Registry Number

Not Available

SMILES

N[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=NC2=C1N=C(N)NC2=O

InChI Identifier

InChI=1S/C10H14N6O4/c11-4-6(18)3(1-17)20-9(4)16-2-13-5-7(16)14-10(12)15-8(5)19/h2-4,6,9,17-18H,1,11H2,(H3,12,14,15,19)/t3-,4-,6-,9-/m1/s1

InChI Key

ROPTVRLUGSPXNH-DXTOWSMRSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine 2'-deoxyribonucleosides. Purine 2'-deoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Purine 2'-deoxyribonucleosides

Direct Parent

Purine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Purine 2'-deoxyribonucleoside
Glycosyl compound
N-glycosyl compound
6-oxopurine
Hypoxanthine
Purinone
Imidazopyrimidine
Purine
Aminopyrimidine
Pyrimidone
N-substituted imidazole
Pyrimidine
Azole
Imidazole
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Secondary alcohol
1,2-aminoalcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Primary aliphatic amine
Alcohol
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Primary alcohol
Organic oxygen compound
Primary amine
Amine
Organonitrogen compound
Organooxygen 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	11.2 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-2.8	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	10.16	ChemAxon
pKa (Strongest Basic)	8.05	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	161.01 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	66.28 m³·mol⁻¹	ChemAxon
Polarizability	26.48 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

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	Proteobacteria	1	Human	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

151665

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

173775

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 2'-amino-2'-deoxyguanosine (MMDBc0007409)

MOL for #<Metabolite:0x00007f2af01fa500>

3D MOL for #<Metabolite:0x00007f2af01fa500>

3D SDF for #<Metabolite:0x00007f2af01fa500>

3D-SDF for #<Metabolite:0x00007f2af01fa500>

PDB for #<Metabolite:0x00007f2af01fa500>

3D PDB for #<Metabolite:0x00007f2af01fa500>

SMILES for #<Metabolite:0x00007f2af01fa500>

INCHI for #<Metabolite:0x00007f2af01fa500>

Structure for #<Metabolite:0x00007f2af01fa500>

3D Structure for #<Metabolite:0x00007f2af01fa500>