NP-MRD: Showing NP-Card for n-[(3r,4r,5r,6r)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid (NP0160922)

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Record Information

Version

2.0

Created at

2022-09-02 18:59:40 UTC

Updated at

2022-09-02 18:59:41 UTC

NP-MRD ID

NP0160922

Secondary Accession Numbers

None

Natural Product Identification

Common Name

n-[(3r,4r,5r,6r)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid

Description

N-acetyl-D-galactosamine, also known as D-galnac or N-acetyl-D-chondrosamine, belongs to the class of organic compounds known as acylaminosugars. These are organic compounds containing a sugar linked to a chain through N-acyl group. N-acetyl-D-galactosamine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. n-[(3r,4r,5r,6r)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid is found in Homo sapiens, Mus musculus and Prunus persica. n-[(3r,4r,5r,6r)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid was first documented in 2022 (PMID: 35961667). Based on a literature review a small amount of articles have been published on N-acetyl-D-galactosamine (PMID: 35887043) (PMID: 35881507) (PMID: 35718742) (PMID: 35694994).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 30  0  0  0  0  0  0  0  0999 V2000
    4.0654    0.8804    0.2315 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6202    0.6254    0.0408 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9402    1.1182   -1.0593 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9929   -0.0646    0.9130 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6094   -0.4048    0.8887 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3221    0.7622    0.8208 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4126    1.9426    0.9248 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0346    0.8224   -0.3720 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8891   -0.2743   -0.5222 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2015    0.0193    0.1274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7320    1.1603   -0.5212 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2693   -1.5679   -0.1259 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5201   -1.9639    1.1647 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2522   -1.3752   -0.2274 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8588   -2.6060   -0.0596 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2969    1.2212    1.2818 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4619    1.6345   -0.4849 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6846   -0.0356    0.0888 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2989    2.0005   -1.4508 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3881   -0.9591    1.8444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0831    0.7390    1.6384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0447    2.6941    0.4762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0868   -0.3370   -1.6340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1228    0.2989    1.1913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9268   -0.7935   -0.0696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1650    1.7733    0.1237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5553   -2.4110   -0.8061 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1487   -1.4293    1.6659 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4301   -0.9372   -1.2303 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7897   -2.5329   -0.4108 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
  9 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 14  5  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  5 20  1  1
  6 21  1  1
  7 22  1  0
  9 23  1  6
 10 24  1  0
 10 25  1  0
 11 26  1  0
 12 27  1  6
 13 28  1  0
 14 29  1  6
 15 30  1  0
M  END


  Mrv1652309022220592D          

 15 15  0  0  1  0            999 V2000
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  4  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  5  4  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  6  0  0  0
 12 14  1  0  0  0  0
  5 14  1  0  0  0  0
 14 15  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0160922

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6+,7-,8?/m1/s1

> <INCHI_KEY>
OVRNDRQMDRJTHS-KEWYIRBNSA-N

> <FORMULA>
C8H15NO6

> <MOLECULAR_WEIGHT>
221.209

> <EXACT_MASS>
221.089937207

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
20.976104827016343

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(3R,4R,5R,6R)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid

> <ALOGPS_LOGP>
-2.31

> <JCHEM_LOGP>
-2.400970284666667

> <ALOGPS_LOGS>
-0.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.71277465937263

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.729937166971195

> <JCHEM_PKA_STRONGEST_BASIC>
1.4620643976553511

> <JCHEM_POLAR_SURFACE_AREA>
122.74000000000002

> <JCHEM_REFRACTIVITY>
47.54639999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.25e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(3R,4R,5R,6R)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   14                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    5   15                                                  
CONECT   15   14                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Value	Source
2-Acetamido-2-deoxy-D-galactose	ChEBI
D-GalNAc	ChEBI
GalNAc	ChEBI
N-Acetyl-D-chondrosamine	ChEBI
WURCS=2.0/1,1,0/[a2112h-1x_1-5_2*ncc/3=o]/1/	ChEBI
2 Acetamido 2 deoxy D galactose	MeSH
2-Acetamido-2-D-galactopyranose	MeSH
Acetylgalactosamine	MeSH
2-Acetamido-2-deoxygalactose	MeSH
N Acetyl D galactosamine	MeSH
2 Acetamido 2 D galactopyranose	MeSH
2 Acetamido 2 deoxygalactose	MeSH

Chemical Formula

C₈H₁₅NO₆

Average Mass

221.2090 Da

Monoisotopic Mass

221.08994 Da

IUPAC Name

N-[(3R,4R,5R,6R)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid

Traditional Name

N-[(3R,4R,5R,6R)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6+,7-,8?/m1/s1

InChI Key

OVRNDRQMDRJTHS-KEWYIRBNSA-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

Species Name	Source	Reference
Homo sapiens	LOTUS Database	35616633
Mus musculus	LOTUS Database	35616633
Prunus persica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as acylaminosugars. These are organic compounds containing a sugar linked to a chain through N-acyl group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Acylaminosugars

Alternative Parents

Substituents

Acylaminosugar
N-acyl-alpha-hexosamine
Hexose monosaccharide
Monosaccharide
Oxane
Acetamide
Carboxamide group
Hemiacetal
Secondary carboxylic acid amide
Secondary alcohol
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Polyol
Alcohol
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Organopnictogen compound
Organonitrogen compound
Primary alcohol
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

N-acetylgalactosamine (CHEBI:28037 )
Amino sugars (C01132 )

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	-2.3	ALOGPS
logP	-2.4	ChemAxon
logS	-0.43	ALOGPS
pKa (Strongest Acidic)	5.73	ChemAxon
pKa (Strongest Basic)	1.46	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	122.74 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	47.55 m³·mol⁻¹	ChemAxon
Polarizability	20.98 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

C00053524

Chemspider ID

32855

KEGG Compound ID

C01132

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

N-Acetylgalactosamine

METLIN ID

Not Available

PubChem Compound

35717

PDB ID

Not Available

ChEBI ID

28037

Good Scents ID

rw1664551

References

General References

Tomnikova A, Kozlik P, Krizek T: Monosaccharide profiling of glycoproteins by capillary electrophoresis with contactless conductivity detection. Electrophoresis. 2022 Oct;43(20):1963-1970. doi: 10.1002/elps.202200033. Epub 2022 Aug 27. [PubMed:35961667 ]
Kato K, Tachibana H: Identification of Multiple Domains of Entamoeba histolytica Intermediate Subunit Lectin-1 with Hemolytic and Cytotoxic Activities. Int J Mol Sci. 2022 Jul 12;23(14):7700. doi: 10.3390/ijms23147700. [PubMed:35887043 ]
Boverio A, Widodo WS, Santema LL, Rozeboom HJ, Xiang R, Guallar V, Mattevi A, Fraaije MW: Structural Elucidation and Engineering of a Bacterial Carbohydrate Oxidase. Biochemistry. 2023 Jan 17;62(2):429-436. doi: 10.1021/acs.biochem.2c00307. Epub 2022 Jul 26. [PubMed:35881507 ]
Zhang S, Cao Z, Fan P, Wang Y, Jia W, Wang L, Wang K, Liu Y, Du X, Hu C, Zhang P, Chen HY, Huang S: A Nanopore-Based Saccharide Sensor. Angew Chem Int Ed Engl. 2022 Aug 15;61(33):e202203769. doi: 10.1002/anie.202203769. Epub 2022 Jul 11. [PubMed:35718742 ]
Cheong CSY, Khan SU, Ahmed N, Narayanan K: Identification of dual active sites in Caenorhabditis elegans GANA-1 protein: an ortholog of the human alpha-GAL a and alpha-NAGA enzymes. J Biomol Struct Dyn. 2023 Jul;41(11):5261-5276. doi: 10.1080/07391102.2022.2084162. Epub 2022 Jun 11. [PubMed:35694994 ]
LOTUS database [Link]

Showing NP-Card for n-[(3r,4r,5r,6r)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid (NP0160922)

MOL for NP0160922 (n-[(3r,4r,5r,6r)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid)

3D MOL for NP0160922 (n-[(3r,4r,5r,6r)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid)

3D SDF for NP0160922 (n-[(3r,4r,5r,6r)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid)

3D-SDF for NP0160922 (n-[(3r,4r,5r,6r)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid)

PDB for NP0160922 (n-[(3r,4r,5r,6r)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid)

3D PDB for NP0160922 (n-[(3r,4r,5r,6r)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid)

SMILES for NP0160922 (n-[(3r,4r,5r,6r)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid)

INCHI for NP0160922 (n-[(3r,4r,5r,6r)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid)

Structure for NP0160922 (n-[(3r,4r,5r,6r)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid)

3D Structure for NP0160922 (n-[(3r,4r,5r,6r)-2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidic acid)