MiMeDB: Showing metabocard for 3-amino-3-deoxy-D-glucose (MMDBc0009544)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 02:02:03 UTC

Update Date

2025-10-07 16:05:37 UTC

Metabolite ID

MMDBc0009544

Metabolite Identification

Common Name

3-amino-3-deoxy-D-glucose

Description

3-amino-3-deoxy-D-glucose is a member of the amino sugar class and is recognized as a metabolite with significant biological implications. This compound, also known as kanosamine, serves as a characteristic sugar unit in kanamycins, a group of aminoglycoside antibiotics (PMID:32237736 ). It plays a crucial role in bacterial cell wall synthesis inhibition, particularly in Staphylococcus aureus, where its growth-inhibitory effects can be countered by glucosamine and N-acetylglucosamine (PMID:479118 ). The antibiotic properties of 3-amino-3-deoxy-D-glucose have been highlighted in studies identifying it as a product of deep-sea bacteria (PMID:3569498 ). Furthermore, it has been investigated alongside various phosphate-modified derivatives to understand its biochemical interactions (PMID:33403742 ). The compound's structural characteristics, including its linkage with other deoxy sugars, underscore its importance in microbial physiology and antibiotic development (PMID:3666956 ). Overall, 3-amino-3-deoxy-D-glucose is a vital metabolite with significant implications in both chemistry and microbiology, particularly in the context of antibiotic resistance and bacterial cell wall synthesis.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152104022D          

 16 15  0  0  1  0            999 V2000
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    1.5395    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    1.5395    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  5  7  1  6  0  0  0
  8  1  2  0  0  0  0
  9  2  1  0  0  0  0
  3 10  1  6  0  0  0
  4 11  1  1  0  0  0
  6 12  1  6  0  0  0
  3 13  1  6  0  0  0
  4 14  1  1  0  0  0
  5 15  1  6  0  0  0
  6 16  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0009544

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(CO)[C@@]([H])(O)[C@]([H])(N)[C@@]([H])(O)C=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H13NO5/c7-5(3(10)1-8)6(12)4(11)2-9/h1,3-6,9-12H,2,7H2/t3-,4+,5+,6+/m0/s1

> <INCHI_KEY>
FOEXHEVNPRRHDY-SLPGGIOYSA-N

> <FORMULA>
C6H13NO5

> <MOLECULAR_WEIGHT>
179.172

> <EXACT_MASS>
179.079372523

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
16.612532292450382

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4S,5R)-3-amino-2,4,5,6-tetrahydroxyhexanal

> <ALOGPS_LOGP>
-2.67

> <JCHEM_LOGP>
-3.6752423596666666

> <ALOGPS_LOGS>
0.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.35112232773319

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.692161107475272

> <JCHEM_PKA_STRONGEST_BASIC>
8.113632439429741

> <JCHEM_POLAR_SURFACE_AREA>
124.01000000000002

> <JCHEM_REFRACTIVITY>
39.003099999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.99e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
kanosamine

> <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       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.645   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.311   2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       3.644   3.644   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0      -0.357   1.334   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       8.978   2.104   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       2.310  -0.206   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       6.311   3.644   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
HETATM   13  H   UNK     0       2.310   2.874   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       6.311   0.564   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       3.644   0.564   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       4.977   2.874   0.000  0.00  0.00           H+0
CONECT    1    3    8                                                       
CONECT    2    4    9                                                       
CONECT    3    1    5   10   13                                             
CONECT    4    2    6   11   14                                             
CONECT    5    3    6    7   15                                             
CONECT    6    4    5   12   16                                             
CONECT    7    5                                                            
CONECT    8    1                                                            
CONECT    9    2                                                            
CONECT   10    3                                                            
CONECT   11    4                                                            
CONECT   12    6                                                            
CONECT   13    3                                                            
CONECT   14    4                                                            
CONECT   15    5                                                            
CONECT   16    6                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

Synonyms

Value	Source
3-Amino-3-deoxyglucose	ChEBI
Aldehydo-kanosamine	ChEBI
D-Kanosamine	ChEBI
Kanosamine	ChEBI

Molecular Formula

C₆H₁₃NO₅

Average Mass

179.172

Monoisotopic Mass

179.079372523

IUPAC Name

(2R,3S,4S,5R)-3-amino-2,4,5,6-tetrahydroxyhexanal

Traditional Name

kanosamine

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CO)[C@@]([H])(O)[C@]([H])(N)[C@@]([H])(O)C=O

InChI Identifier

InChI=1S/C6H13NO5/c7-5(3(10)1-8)6(12)4(11)2-9/h1,3-6,9-12H,2,7H2/t3-,4+,5+,6+/m0/s1

InChI Key

FOEXHEVNPRRHDY-SLPGGIOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hexoses. These are monosaccharides in which the sugar unit is a is a six-carbon containing moeity.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Hexoses

Alternative Parents

Substituents

Hexose monosaccharide
1,3-aminoalcohol
Alpha-hydroxyaldehyde
1,2-aminoalcohol
Secondary alcohol
Polyol
Organic nitrogen compound
Primary amine
Primary alcohol
Hydrocarbon derivative
Organonitrogen compound
Primary aliphatic amine
Organic oxide
Carbonyl group
Amine
Aldehyde
Alcohol
Organopnictogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

D-kanosamine (CHEBI:31747 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	199 g/L	ALOGPS
logP	-2.7	ALOGPS
logP	-3.7	ChemAxon
logS	0.05	ALOGPS
pKa (Strongest Acidic)	12.69	ChemAxon
pKa (Strongest Basic)	8.11	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	124.01 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	39 m³·mol⁻¹	ChemAxon
Polarizability	16.61 Å³	ChemAxon
Number of Rings	0	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/Eubacteria	Firmicutes	1		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

144368

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

164683

PDB ID

Not Available

ChEBI ID

31747

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 3-amino-3-deoxy-D-glucose (MMDBc0009544)

MOL for #<Metabolite:0x00007f2acc220c88>

3D MOL for #<Metabolite:0x00007f2acc220c88>

3D SDF for #<Metabolite:0x00007f2acc220c88>

3D-SDF for #<Metabolite:0x00007f2acc220c88>

PDB for #<Metabolite:0x00007f2acc220c88>

3D PDB for #<Metabolite:0x00007f2acc220c88>

SMILES for #<Metabolite:0x00007f2acc220c88>

INCHI for #<Metabolite:0x00007f2acc220c88>

Structure for #<Metabolite:0x00007f2acc220c88>

3D Structure for #<Metabolite:0x00007f2acc220c88>