MiMeDB: Showing metabocard for Oxetanocin (MMDBc0020839)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 10:59:22 UTC

Update Date

2025-10-07 16:07:07 UTC

Metabolite ID

MMDBc0020839

Metabolite Identification

Common Name

Oxetanocin

Description

Oxetanocin is a member of the nucleoside chemical class, specifically characterized by its oxetane moiety. This compound is involved in the biosynthesis of oxetane nucleosides, such as oxetanocin A and albucidin, through pathways catalyzed by B12-dependent radical S-adenosyl-l-methionine (SAM) enzymes, notably AlsB and OxsB (PMID:40643284 ). Oxetanocin undergoes nonenzymatic decomposition but can be converted to oxetanocin A aldehyde phosphate or albucidin phosphate in the presence of specific enzymes, thereby completing the biosynthetic pathways for these compounds (PMID:40643284 ). The total synthesis of oxetanocin A has been achieved, highlighting its significance as an antiviral natural product (PMID:38011311 ). OxsB catalyzes the oxidative ring contraction of 2'-deoxyadenosine 5'-phosphate to form the oxetane-containing precursor of oxetanocin A phosphate (PMID:36719327 ). While the biosynthesis of oxetanocin A is well-documented, the pathways for albucidin remain less understood (PMID:36064953 ). Oxetanocin A, an oxetanosyl N-glycoside nucleoside, was first isolated from Bacillus megaterium in 1986, further emphasizing its relevance in natural product chemistry (PMID:36054994 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152112592D          

 21 23  0  0  1  0            999 V2000
   -0.6359   -0.0487    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2683   -1.8234    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
    0.1487   -0.3037    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5232   -1.0387    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
    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
    2.6378    3.1729    0.0000 N   0  0  0  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
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8074    0.7583    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8203   -2.4365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2583   -0.6642    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3871   -0.9310    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1506   -1.5745    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7062    0.1356    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  1  0  0  0
  6  2  1  6  0  0  0
  6  5  1  0  0  0  0
  8  7  2  0  0  0  0
  9  7  1  0  0  0  0
 10  5  1  0  0  0  0
 11  8  1  0  0  0  0
 12  3  2  0  0  0  0
 12  8  1  0  0  0  0
 13  3  1  0  0  0  0
 13  9  2  0  0  0  0
 14  4  2  0  0  0  0
 14  7  1  0  0  0  0
 15  4  1  0  0  0  0
 15  9  1  0  0  0  0
 10 15  1  6  0  0  0
 16  1  1  0  0  0  0
 17  2  1  0  0  0  0
 18  6  1  0  0  0  0
 18 10  1  0  0  0  0
  5 19  1  6  0  0  0
  6 20  1  1  0  0  0
 10 21  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0020839

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H13N5O3/c11-8-7-9(13-3-12-8)15(4-14-7)10-5(1-16)6(2-17)18-10/h3-6,10,16-17H,1-2H2,(H2,11,12,13)/t5-,6-,10-/m1/s1

> <INCHI_KEY>
LMJVXGOFWKVXAW-OXOINMOOSA-N

> <FORMULA>
C10H13N5O3

> <MOLECULAR_WEIGHT>
251.246

> <EXACT_MASS>
251.101839299

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
24.39871441052933

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3R,4S)-2-(6-amino-9H-purin-9-yl)-4-(hydroxymethyl)oxetan-3-yl]methanol

> <ALOGPS_LOGP>
-0.70

> <JCHEM_LOGP>
-1.6488466910000001

> <ALOGPS_LOGS>
-1.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.353041759734499

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.554061199314209

> <JCHEM_PKA_STRONGEST_BASIC>
3.9378813694005905

> <JCHEM_POLAR_SURFACE_AREA>
119.31000000000002

> <JCHEM_REFRACTIVITY>
62.1203

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.05e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3R,4S)-2-(6-aminopurin-9-yl)-4-(hydroxymethyl)oxetan-3-yl]methanol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0      -1.187  -0.091   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.501  -3.404   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.278  -0.567   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.977  -1.939   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       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       4.924   5.923   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       6.258   3.613   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       4.924   1.303   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0      -1.507   1.415   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       1.531  -4.548   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       2.349  -1.240   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0      -0.723  -1.738   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       2.148  -2.939   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       3.185   0.253   0.000  0.00  0.00           H+0
CONECT    1    5   16                                                       
CONECT    2    6   17                                                       
CONECT    3   12   13                                                       
CONECT    4   14   15                                                       
CONECT    5    1    6   10   19                                             
CONECT    6    2    5   18   20                                             
CONECT    7    8    9   14                                                  
CONECT    8    7   11   12                                                  
CONECT    9    7   13   15                                                  
CONECT   10    5   15   18   21                                             
CONECT   11    8                                                            
CONECT   12    3    8                                                       
CONECT   13    3    9                                                       
CONECT   14    4    7                                                       
CONECT   15    4    9   10                                                  
CONECT   16    1                                                            
CONECT   17    2                                                            
CONECT   18    6   10                                                       
CONECT   19    5                                                            
CONECT   20    6                                                            
CONECT   21   10                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

Synonyms

Value	Source
(-)-Oxetanocin	ChEBI
(-)-Oxetanocin a	ChEBI
9-((2'r,3'r,4's)-3',4'-Bis(hydroxymethyl)-2'-oxetanyl)adenine	ChEBI
9-[(2R,3R,4S)-3,4-Bis(hydroxymethyl)-2-oxetanyl]adenine	ChEBI
NK 84-0218	ChEBI
Oxetanocin	ChEBI
9-(3,4-Bis(hydroxymethyl)-2-oxetanyl)adenine	MeSH

Molecular Formula

C₁₀H₁₃N₅O₃

Average Mass

251.246

Monoisotopic Mass

251.101839299

IUPAC Name

[(2R,3R,4S)-2-(6-amino-9H-purin-9-yl)-4-(hydroxymethyl)oxetan-3-yl]methanol

Traditional Name

[(2R,3R,4S)-2-(6-aminopurin-9-yl)-4-(hydroxymethyl)oxetan-3-yl]methanol

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C10H13N5O3/c11-8-7-9(13-3-12-8)15(4-14-7)10-5(1-16)6(2-17)18-10/h3-6,10,16-17H,1-2H2,(H2,11,12,13)/t5-,6-,10-/m1/s1

InChI Key

LMJVXGOFWKVXAW-OXOINMOOSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 6-aminopurines. These are purines that carry an amino group at position 6. Purine is a bicyclic aromatic compound made up of a pyrimidine ring fused to an imidazole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Imidazopyrimidines

Sub Class

Purines and purine derivatives

Direct Parent

6-aminopurines

Alternative Parents

Substituents

6-aminopurine
Aminopyrimidine
N-substituted imidazole
Imidolactam
Pyrimidine
Azole
Imidazole
Heteroaromatic compound
Oxetane
Oxacycle
Azacycle
Alcohol
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic oxygen compound
Amine
Primary alcohol
Primary amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

primary alcohol (CHEBI:86012 )
diol (CHEBI:86012 )
nucleoside analogue (CHEBI:86012 )
oxetanes (CHEBI:86012 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	10.5 g/L	ALOGPS
logP	-0.7	ALOGPS
logP	-1.6	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	14.55	ChemAxon
pKa (Strongest Basic)	3.94	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	119.31 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	62.12 m³·mol⁻¹	ChemAxon
Polarizability	24.4 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

Not Available

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	Firmicutes	2	Human feces; 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

C00017819

Chemspider ID

65182

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

72214

PDB ID

Not Available

ChEBI ID

86012

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 Oxetanocin (MMDBc0020839)

MOL for #<Metabolite:0x00007f8dbcfa7520>

3D MOL for #<Metabolite:0x00007f8dbcfa7520>

3D SDF for #<Metabolite:0x00007f8dbcfa7520>

3D-SDF for #<Metabolite:0x00007f8dbcfa7520>

PDB for #<Metabolite:0x00007f8dbcfa7520>

3D PDB for #<Metabolite:0x00007f8dbcfa7520>

SMILES for #<Metabolite:0x00007f8dbcfa7520>

INCHI for #<Metabolite:0x00007f8dbcfa7520>

Structure for #<Metabolite:0x00007f8dbcfa7520>

3D Structure for #<Metabolite:0x00007f8dbcfa7520>