NP-MRD: Showing NP-Card for (3r,4s,5s,6r)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol (NP0318148)

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Record Information

Version

2.0

Created at

2022-09-11 18:28:28 UTC

Updated at

2022-09-11 18:28:29 UTC

NP-MRD ID

NP0318148

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r,4s,5s,6r)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol

Description

(3r,4s,5s,6r)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol was first documented in 1966 (PMID: 4959563).

Structure

MOL 3D MOL SDF PDB SMILES InChI

 
  Mrv1533006051515532D          
 
 12 12  0  0  1  0            999 V2000
   18.2732  -10.2618    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5589  -10.6706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8481  -10.2618    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5589  -11.4958    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.1339  -10.6706    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.8481  -11.9088    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.2732  -11.9088    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.1339  -11.4958    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.4196  -10.2618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8481  -12.7340    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.4196  -11.9088    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.7097  -10.6706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  4  7  1  6  0  0  0
  5  8  1  0  0  0  0
  5  9  1  1  0  0  0
  6 10  1  1  0  0  0
  8 11  1  6  0  0  0
  9 12  1  0  0  0  0
  6  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0318148

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H]1[C@@H](O)C(O)O[C@H](CO)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H13NO5/c7-3-4(9)2(1-8)12-6(11)5(3)10/h2-6,8-11H,1,7H2/t2-,3+,4-,5-,6?/m1/s1

> <INCHI_KEY>
BQCCAEOLPYCBAE-CBPJZXOFSA-N

> <FORMULA>
C6H13NO5

> <MOLECULAR_WEIGHT>
179.172

> <EXACT_MASS>
179.079372523

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
16.48774974655726

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5S,6R)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol

> <ALOGPS_LOGP>
-2.74

> <JCHEM_LOGP>
-3.0394210146666665

> <ALOGPS_LOGS>
0.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.22959159738732

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.367382583606513

> <JCHEM_PKA_STRONGEST_BASIC>
8.511687591997841

> <JCHEM_POLAR_SURFACE_AREA>
116.17

> <JCHEM_REFRACTIVITY>
37.58089999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.42e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,4S,5S,6R)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-JUN-15         0                                  
HETATM    1  O   UNK     0      34.110 -19.155   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      32.777 -19.919   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      31.450 -19.155   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      32.777 -21.459   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      30.117 -19.919   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      31.450 -22.230   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      34.110 -22.230   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      30.117 -21.459   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      28.783 -19.155   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      31.450 -23.770   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0      28.783 -22.230   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      27.458 -19.919   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2    5                                                       
CONECT    4    2    6    7                                                  
CONECT    5    3    8    9                                                  
CONECT    6    4   10    8                                                  
CONECT    7    4                                                            
CONECT    8    5   11    6                                                  
CONECT    9    5   12                                                       
CONECT   10    6                                                            
CONECT   11    8                                                            
CONECT   12    9                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

View in JSmol

Synonyms

Value	Source
D-Kanosamine	ChEBI
Kanosamine	ChEBI
3-Amino-3-deoxy-D-glucose	Kegg
3-amino-3-Deoxyglucose	MeSH

Chemical Formula

C₆H₁₃NO₅

Average Mass

179.1720 Da

Monoisotopic Mass

179.07937 Da

IUPAC Name

(3R,4S,5S,6R)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol

Traditional Name

(3R,4S,5S,6R)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol

CAS Registry Number

Not Available

SMILES

N[C@@H]1[C@@H](O)C(O)O[C@H](CO)[C@H]1O

InChI Identifier

InChI=1S/C6H13NO5/c7-3-4(9)2(1-8)12-6(11)5(3)10/h2-6,8-11H,1,7H2/t2-,3+,4-,5-,6?/m1/s1

InChI Key

BQCCAEOLPYCBAE-CBPJZXOFSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

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
Amino saccharide
Oxane
1,2-aminoalcohol
Hemiacetal
Secondary alcohol
Polyol
Organoheterocyclic compound
Oxacycle
Primary amine
Primary alcohol
Organopnictogen compound
Organonitrogen compound
Primary aliphatic amine
Organic nitrogen compound
Alcohol
Amine
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

D-kanosamine (CHEBI:72725 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-2.7	ALOGPS
logP	-3	ChemAxon
logS	0.48	ALOGPS
pKa (Strongest Acidic)	11.37	ChemAxon
pKa (Strongest Basic)	8.51	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	116.17 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	37.58 m³·mol⁻¹	ChemAxon
Polarizability	16.49 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00018737

Chemspider ID

Not Available

KEGG Compound ID

C12212

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

443709

PDB ID

Not Available

ChEBI ID

72725

Good Scents ID

Not Available

References

General References

Milner JL, Silo-Suh L, Lee JC, He H, Clardy J, Handelsman J: Production of kanosamine by Bacillus cereus UW85. Appl Environ Microbiol. 1996 Aug;62(8):3061-5. doi: 10.1128/AEM.62.8.3061-3065.1996. [PubMed:8702302 ]
Janiak AM, Milewski S: Mechanism of antifungal action of kanosamine. Med Mycol. 2001 Oct;39(5):401-8. doi: 10.1080/mmy.39.5.401.408. [PubMed:12054050 ]
Guo J, Frost JW: Kanosamine biosynthesis: a likely source of the aminoshikimate pathway's nitrogen atom. J Am Chem Soc. 2002 Sep 11;124(36):10642-3. doi: 10.1021/ja026628m. [PubMed:12207504 ]
Arakawa K, Muller R, Mahmud T, Yu TW, Floss HG: Characterization of the early stage aminoshikimate pathway in the formation of 3-amino-5-hydroxybenzoic acid: the RifN protein specifically converts kanosamine into kanosamine 6-phosphate. J Am Chem Soc. 2002 Sep 11;124(36):10644-5. doi: 10.1021/ja0206339. [PubMed:12207505 ]
Meyer zu Reckendorf W: A simple synthesis of 3-amino-3-deoxy-D-glucose (kanosamine). Angew Chem Int Ed Engl. 1966 Nov;5(11):967. doi: 10.1002/anie.196609671. [PubMed:4959563 ]
LOTUS database [Link]

Showing NP-Card for (3r,4s,5s,6r)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol (NP0318148)

MOL for NP0318148 ((3r,4s,5s,6r)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol)

3D MOL for NP0318148 ((3r,4s,5s,6r)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol)

3D SDF for NP0318148 ((3r,4s,5s,6r)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol)

3D-SDF for NP0318148 ((3r,4s,5s,6r)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol)

PDB for NP0318148 ((3r,4s,5s,6r)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol)

3D PDB for NP0318148 ((3r,4s,5s,6r)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol)

SMILES for NP0318148 ((3r,4s,5s,6r)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol)

INCHI for NP0318148 ((3r,4s,5s,6r)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol)

Structure for NP0318148 ((3r,4s,5s,6r)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol)

3D Structure for NP0318148 ((3r,4s,5s,6r)-4-amino-6-(hydroxymethyl)oxane-2,3,5-triol)