NP-MRD: Showing NP-Card for D-Glucosaminide (NP0087170)

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Record Information

Version

2.0

Created at

2022-05-11 16:42:05 UTC

Updated at

2022-05-11 16:42:05 UTC

NP-MRD ID

NP0087170

Secondary Accession Numbers

None

Natural Product Identification

Common Name

D-Glucosaminide

Description

D-Glucosaminide belongs to the class of organic compounds known as oligosaccharides. These are carbohydrates made up of 3 to 10 monosaccharide units linked to each other through glycosidic bonds. D-Glucosaminide is a very strong basic compound (based on its pKa). D-Glucosaminide was first documented in 1981 (PMID: 7237781). D-Glucosaminide is an intermediate in the Human Aminosugars metabolism, the substrate of the enzyme di-N-acetyl-chitobiase , from the Glycosidases class (i.E.: Enzymes hydrolyzing O- and S-glycosyl compounds) (PMID: 12705338) (PMID: 3255304).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02231219552D          

 34 36  0  0  1  0            999 V2000
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   29.3888   -8.7128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.6743  -14.0754    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.6743   -7.4752    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv0541 02231219552D          

 34 36  0  0  1  0            999 V2000
   25.8164   -9.1253    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0087170

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@H]1[C@H](O)O[C@H](CO)[C@@H](OC2O[C@H](CO)C(O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3N)[C@H](O)[C@H]2N)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C18H35N3O13/c19-7-12(27)14(5(2-23)30-16(7)29)33-18-9(21)13(28)15(6(3-24)32-18)34-17-8(20)11(26)10(25)4(1-22)31-17/h4-18,22-29H,1-3,19-21H2/t4-,5-,6-,7-,8-,9-,10-,11-,12-,13-,14-,15?,16-,17+,18?/m1/s1

> <INCHI_KEY>
RQFQJYYMBWVMQG-KAPKVSAKSA-N

> <FORMULA>
C18H35N3O13

> <MOLECULAR_WEIGHT>
501.4828

> <EXACT_MASS>
501.216988221

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
48.416793379144636

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R,5S,6R)-3-amino-5-{[(3R,4R,6R)-3-amino-5-{[(2S,3R,4R,5S,6R)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-6-(hydroxymethyl)oxane-2,4-diol

> <ALOGPS_LOGP>
-3.03

> <JCHEM_LOGP>
-6.794855899333335

> <ALOGPS_LOGS>
-0.34

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
3

> <JCHEM_PKA>
12.732558023282717

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.7099647552811

> <JCHEM_PKA_STRONGEST_BASIC>
8.866550974871195

> <JCHEM_POLAR_SURFACE_AREA>
286.04999999999995

> <JCHEM_REFRACTIVITY>
105.72249999999991

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.29e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-glucosaminide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      48.191 -17.034   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      48.191 -23.194   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      52.192 -19.344   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      52.192 -20.884   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      54.859 -16.264   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      53.525 -26.274   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      53.525 -13.954   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      45.523 -18.574   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      50.858 -12.414   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      48.191 -26.274   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      49.524 -20.884   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      52.192 -23.964   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      50.858 -17.034   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0      45.523 -21.654   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0      48.191 -13.954   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      50.858 -27.814   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      50.858 -18.574   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      50.858 -21.654   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      53.525 -17.034   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      48.191 -21.654   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      49.524 -16.264   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      52.192 -25.504   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      49.524 -19.344   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      50.858 -23.194   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      52.192 -16.264   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      48.191 -18.574   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      49.524 -23.964   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      52.192 -14.724   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      46.857 -19.344   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      50.858 -13.954   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      49.524 -25.504   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      46.857 -20.884   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      49.524 -14.724   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      50.858 -26.274   0.000  0.00  0.00           C+0
CONECT    1   21   26                                                       
CONECT    2   20   27                                                       
CONECT    3   17                                                            
CONECT    4   18                                                            
CONECT    5   19                                                            
CONECT    6   22                                                            
CONECT    7   28                                                            
CONECT    8   29                                                            
CONECT    9   30                                                            
CONECT   10   31                                                            
CONECT   11   20   23                                                       
CONECT   12   22   24                                                       
CONECT   13   21   25                                                       
CONECT   14   32                                                            
CONECT   15   33                                                            
CONECT   16   34                                                            
CONECT   17    3   23                                                       
CONECT   18    4   24                                                       
CONECT   19    5   25                                                       
CONECT   20    2   11   32                                                  
CONECT   21    1   13   33                                                  
CONECT   22    6   12   34                                                  
CONECT   23   11   17   26                                                  
CONECT   24   12   18   27                                                  
CONECT   25   13   19   28                                                  
CONECT   26    1   23   29                                                  
CONECT   27    2   24   31                                                  
CONECT   28    7   25   30                                                  
CONECT   29    8   26   32                                                  
CONECT   30    9   28   33                                                  
CONECT   31   10   27   34                                                  
CONECT   32   14   20   29                                                  
CONECT   33   15   21   30                                                  
CONECT   34   16   22   31                                                  
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

View in JSmol

Synonyms

Value	Source
4,5-Dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-4-hydroxy-6-(hydroxymethyl)oxa	HMDB
N-2-yl]Oxy-6-(hydroxymethyl)oxane-2,4-diol	HMDB

Chemical Formula

C₁₈H₃₅N₃O₁₃

Average Mass

501.4828 Da

Monoisotopic Mass

501.21699 Da

IUPAC Name

(2R,3R,4R,5S,6R)-3-amino-5-{[(3R,4R,6R)-3-amino-5-{[(2S,3R,4R,5S,6R)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-6-(hydroxymethyl)oxane-2,4-diol

Traditional Name

D-glucosaminide

CAS Registry Number

Not Available

SMILES

N[C@H]1[C@H](O)O[C@H](CO)[C@@H](OC2O[C@H](CO)C(O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3N)[C@H](O)[C@H]2N)[C@@H]1O

InChI Identifier

InChI=1S/C18H35N3O13/c19-7-12(27)14(5(2-23)30-16(7)29)33-18-9(21)13(28)15(6(3-24)32-18)34-17-8(20)11(26)10(25)4(1-22)31-17/h4-18,22-29H,1-3,19-21H2/t4-,5-,6-,7-,8-,9-,10-,11-,12-,13-,14-,15?,16-,17+,18?/m1/s1

InChI Key

RQFQJYYMBWVMQG-KAPKVSAKSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oligosaccharides. These are carbohydrates made up of 3 to 10 monosaccharide units linked to each other through glycosidic bonds.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Oligosaccharides

Alternative Parents

Substituents

Oligosaccharide
Aminoglycoside core
Glycosyl compound
O-glycosyl compound
Amino saccharide
Oxane
1,2-aminoalcohol
Secondary alcohol
Hemiacetal
Organoheterocyclic compound
Acetal
Oxacycle
Primary amine
Hydrocarbon derivative
Primary aliphatic amine
Organonitrogen compound
Organopnictogen compound
Organic nitrogen compound
Amine
Alcohol
Primary alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

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	-3	ALOGPS
logP	-6.8	ChemAxon
logS	-0.34	ALOGPS
pKa (Strongest Acidic)	11.71	ChemAxon
pKa (Strongest Basic)	8.87	ChemAxon
Physiological Charge	3	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	286.05 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	105.72 m³·mol⁻¹	ChemAxon
Polarizability	48.42 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

HMDB0004270

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB023358

KNApSAcK ID

Not Available

Chemspider ID

389715

KEGG Compound ID

C06023

BioCyc ID

CPD-7177

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

7043

PubChem Compound

440883

PDB ID

Not Available

ChEBI ID

35373

Good Scents ID

Not Available

References

General References

Horak E, Hopfer SM, Sunderman FW Jr: Spectrophotometric assay for urinary N-acetyl-beta-D-glucosaminidase activity. Clin Chem. 1981 Jul;27(7):1180-5. [PubMed:7237781 ]
Hermida J, Casal JA, Tutor JC: Effect of partial proteolysis on the activation energy of beta-n-acetylhexosaminidase precursor and mature forms. Clin Chem Lab Med. 2003 Mar;41(3):302-5. doi: 10.1515/CCLM.2003.048. [PubMed:12705338 ]
Makise J, Saito E, Obuchi M, Kanayama M, Ichikawa K, Harakawa K, Yoshida K: Kinetic rate assay of urinary N-acetyl-beta-D-glucosaminidase with 2-chloro-4-nitrophenyl-N-acetyl-beta-D-glucosaminide as substrate. Clin Chem. 1988 Oct;34(10):2140-3. [PubMed:3255304 ]

Showing NP-Card for D-Glucosaminide (NP0087170)

MOL for NP0087170 (D-Glucosaminide)

3D MOL for NP0087170 (D-Glucosaminide)

3D SDF for NP0087170 (D-Glucosaminide)

3D-SDF for NP0087170 (D-Glucosaminide)

PDB for NP0087170 (D-Glucosaminide)

3D PDB for NP0087170 (D-Glucosaminide)

SMILES for NP0087170 (D-Glucosaminide)

INCHI for NP0087170 (D-Glucosaminide)

Structure for NP0087170 (D-Glucosaminide)

3D Structure for NP0087170 (D-Glucosaminide)